Gold is the best. It has the most stuff in it and all of the old pokemon with some new ones that were all fairly imaginative. Also breeding was pro.

Bonus:
CHARIZARD. OF FUCKING COURSE.

This is difficult - G/S are so much different mechanics-wise than HG/SS.

I'm going to have to give best game to Platinum, because of that generation's most essential addition - the physical/special split. It's now near impossible to go back and play anything before this gen intelligently.

Bonus: My favorite RAPIDASH... It's...cute...lovely...smart...plus...amazing...you think so?...oh yes...it's...stunning...kindly...love it! Hug it...when...sleeping...warm and cuddly...spectacular...ravishing...

RED/BLUE

VOTERS FOR THE OTHERS ARE INFIDELS AND MUST BE KILLED

gold and silver it had both regions which was awsome but the lack of it in other once kind of dissapointed me ( i was excepcting after hoenn to go back to johoto )

bonus question infernape

Ruby/ Sapphire were the best to me mainly for one reason, the music in Littleroot Town. And Bulbasaur is by far the best Pokemon of all time.

2nd Gen, it was originally such an improvement (read : a true sequel) to the 1st gen games... And then the remakes took everything that made it great and added more new great features.

Also : SoulSilver > HeartGold

Bonus : I actually like Ampharos a lot, it's easy to get in the early game yet it's surprisingly good! Scizor is also a favorite.

The Best games in the series are by far, Gold/Silver, especially the remakes.
What are my reasons?
- 100 more pokemon whit an awesome design.
- Compared with the others games, they has the best innovations (the breeding, more kinds of pokeballs, two maps, you can battle again with a trainer that we had defeated, the battle tower in Pokemon Crystal, etc)

Bonus: By far, the best pokemon off the entire series is Tyranitar.

Excuse my bad english, i'm from Argentina.
Greetings

I have the best memories of playing crystal but lets face it, Gen II does not stand up to Gen IV in terms of gameplay, so my vote goes to Platinum. Also, I wish you would count the votes differently. My true favorite is Soul Silver because of all the enhancements, but I can't vote that way since it would count as a vote for Gen II.

HeartGold/Soulsilver

These games were masterpieces. I even played it in Japanese before it came out and it was still better than Ruby/Saphirre, even if I could only read battle text (FUCK berry blocks and beauty contests).

BONUS: GEODUDE the suicide bomber of Pokemon

Gold and Silver were by far the absolute BEST addition to the series because no other generation felt like such a humongous upgrade. G/S had it all: day and night, Johto and Kanto, fighting Ash, and perhaps the best addition of Pokemon out of all of the sequels.

Bonus: I love Teddiursa and Ursaring, I have no idea why, but on a replay of Gold, I caught one and just decided to raise it. Now I have a level 100 Ursaring in my Diamond / HG ^^

at heart i'm a gold fan,

but I did love pearl

Bonus:

Luxray, which is why i love pearl, a dark/electric was ridiculous. I basically shunned my starter and raised luxray.

My favourite is the G/S/C series, with the remakes being my favourite of those games. It had an enormous amount of upgrades: The pokegear, exp bar, 101 new pokemons, 16 gym leaders, two continents, two new types, and the night and day system - It simply was the best sequel ever!

Bonus: Gyarados, because it's powerful badass of a pokemon, and because of the imense satisfaction of getting one after having to train up a useless Magikarp.

Ruby, a lot of extra things that kept me coming back and playing the game for over 300 hours.

Bulbasaur.

Pokemon Crystal
it was the first one you could play as a girl
and the Cartridge was clear that was awesome back then
Bonus:NidoKing is my Homeboy

Whoops forgot mah bonus: Sandslash has been my favorite since I first laid eyes on him. Rhydon would be a close second for me. If I were a gym leader I would totally be ground type.

Pokemon red/blue. How could it not be the best, before we even knew what to expect. I had no idea about eevee's multiple forms, no idea that nidorina had sex specific evolutions, no idea how the story was going to end. Even the 8 gym thig was novel.

My favorite pokemon evolution was the abra- kadabra-alakazam

Yeah, I'm gonna join the popular crowd and say Gold/Silver.

(H)G/(S)S/C
The pinnacle of Pokemon.

I JUST started back into Pokeymans again with HG, and plan to play Black (The last I played was Yellow). So my vote goes to gold, with all the stuff they improved upon the series.

Bonus: My favorite is Koffing/Weezing because it's a total bad-guy pokeyman. My favorite evolution is Magikarp/Gyarados, because... Well... You totally don't expect it.

Pokemon Yellow. It was the game that I spent the most time with. My parents wouldn't let me buy any of the second gen series and I didn't know about emulators back then. Around that time I just stopped (grew outta that phase.) Around the beginning of college, I got back into it with Pokemon Emerald. Still haven't beat it yet. I have a feeling that the Elite 4 is rigged ( my pokemon are only 2-3 levels above their pokemon :) ) I dabbled in the DS games but what's up with the speed? The trainer walks so slowly and it seems kinda sluggish. The touch controls are great during the battles though (speeds up everything!) I haven't tried Soul Silver or Heart Gold yet so hopefully they fixed that. I'm really looking forward to Black & White also. It's surprising that I'm actually anxious to see the new pokemon after all these years.

Bonus Question: favorite pokemon would be Diglett, and favorite evolution would be Eevee since there are a shit ton of options. I was there for the original 3 and there are now what? 7?!

Obviously Gold and Silver. Best sequels in the Pokemon series thus far. Lots of new features and lots of improvements from the previous games. No other Pokemon game has done that again.

Silver

Oh, sorta tough call. RBY/RGBY had THE classic air (and a sinister air, what with Lavender Town in particular), and Yellow was my first (and most). GSC (well, Gold and HeartGold; may one day should play Crystal) also had the GB/C sensibilities of doing much with little, unlike RSE, whose music hurt me inside because they chose such wrong noises for the tunes, but playing HG, Team Rocket's much more tagalong, and the DS script makes me feel dissatisfied, like a weak copypasta (also, his name is fuggin' Green, it fits him, eff Blue (literally, if we're talking Adventures/Special). Emerald, though, was may second win, and overall Hoenn was lively. I haven't gotten far in Platinum, but the script is excelsior (I'm told it was done by a Something Awful forum member); I especially liked Barry's spelling of P-O-K-accent-E Balls! However, it falls into the menu trappings of RSE; HGSS improved things so. damn. much., although it lost the Match Call function from Emerald.

So, in the end... I'm leaning toward HeartGold for ease of play, Platinum for its script and characterization (seeing Gym Leaders outside of their Gyms, even unto HGSS!). My loyalties, though, are with Yellow and Emerald, so...

...

BLACK AND WHITE VERSIONS

(Okay, fine, the "third game" of those two; Gray? Monochrome? Sepia? Pea Green?)

HeartGold/SoulSilver

Bonus: Wooper

(It'd be awesome if you counted the bonus answers to see which Pokemon's the most popular here).

Pokemon Gold.

It made the most advances to the game without giving you the headache of figuring out EVs, and Natures, and all that other crap that Ruby introduced.
The Day/Night system was great, and the pokemon designs were still believable. I have a few hundred hours logged in my copy of Gold,and I'm still waiting to get Heart Gold (I want to beat Emerald first(I stopped playing about 6 years ago)).


Bonus question I have a two:
My Umberon can kick serious ass
My Mewtwo was/is unstoppable

I consider Yellow it's own and best!

Silver/Soul Silver. It had Lugia in it, better than a bird that has "ho" and its reversal in its name.

But in seriousness, that game really opened the door to a lot of innovation in the pokemon series that hasn't really been seen since...well, those games. Sure, you have online play and more pokemon now, but not only were stats and battling simpler then, a lot of the things Silver and Gold created have just been expanded on in some alternate method (pokegear evolving to other things). Not to mention the night and day thing too.

The most innovation I've seen in the series is the upcoming one...but it will be tough to beat Silver in my mind. (Crystal was cool, if only for the Suicune sub-story)

As much I am in love with the previous entries, Pokemon HeartGold/SoulSilver. It grabbed everything that was great from the original entries and made it even better!

I'm loving Soul Silver because its ability to channel the awesome of the original g/s/c (my previous favorites) combined with all the improvements modern pokeymen bring to the table (like running).

Bonus:

Motherfucking Tyranitar or Porygon-Z

Gold!!!
Miltank is the best Pokemon BY FAR

Heart Gold/Soul Silver. Took the best Pokemon series of all time and improved it a bunch. Even if we were to look at just G/S, it was still one of the best generation. It had new Pokemon that were reasonable additions (I rarely, if ever, see anyone complaining about Generation 2 Pokemon) and the day/night system was an awesome aspect that for some reason, was never reimplemented.

Bonus: Scyther. I loved Scyther since the beginning, if just because he was a Pokemon with fucking swords for hands. And then Scizor because Technician/Sword Dance/Bullet Punch completely destroys.

Red!

Bonus: MissingNo

pokemon red and blue.

The Pokenazi in me wants to say that this should be divided into generations instead of the way it is, but I will just have to take my lumps and say Soul Silver, since it is the true supremacy, what with having your 'mons follow you around. Also really enjoyed that Voltorb game. Who would think that Europe getting everyone else censored would be a good thing!

Bonus Question=The new grass starter Tsutarja, since he seems like he could evolve into something badass.

Snap.
Because it was actually fun. Oh, Snap!

...Yeah, I had to go there.
I played Leafgreen 2-3 years ago and didn't care enough to actually beat the elite four. Grinding is tedious, the gameplay isn't that fun, and the monsters don't even animate well enough to be entertaining in that regard.
When they make an action/RPG open world Pokemon game for a console, I'll jump aboard and give it another try. As is though, I've actually enjoyed Snap! more than any of the other games.

Bonus question: Snorlax. Giant fluffy self-healing beanbag chair.

Red/Blue/Yellow

Bonus: the Eevees

Silver because after you got through the Johto region you could go back to Kanto. Soul Silver is a sweet remake.
Bonus: Gengar is the best pokemon!

Gold / Silver/ Crystal wins for me because you can go back to the original region (Kanto) as well.

Gold and Silver. I stopped playing the games after those, because I felt I did everything I needed to. 10 years later, Heart Gold and Soul Silver convinced me I needed to start it up again.

Bonus question: Alakazam.

Pokemon Gold/Silver

Favorite Pokemon? Arcanine, of course.
It's a giant dog mixed with a tiger and a lion and it also breathes fire. Its pre-evolution is a puppy for God sakes. How can it not be the most awesome pokemon EVER?

Mystery Dungeon, 2 Explorers of Sky in specific. HOLY CRAP SPINOFF TITLE NO ONE LIKES
But me.

Why? You can get 492 Pokemon on your team without trading (not that you can) and any Pokemon, ANY Pokemon can get max stats if you work for it. Not to mention the moves make sense too. Instead of the regular Pokemon battles where both sides just beat each other up without any semblance of distance (on the handhelds), distance and range and area of effect matters for moves. Thunderbolt is a pretty standard attack in the regular games, right? In PMD, it hits the eight tiles around the user. Shock Wave will actually go as far as eight tiles in a single line. Quick Attack hits from two tiles away and allows you to attack safely through your allies.

Then there's the fact that you can have four Pokemon on your team at a time, size ratings notwithstanding. Then there's the fact that there are no humans. I mean, they're mentioned in the story, but you're not some fresh-from-diapers kid wandering the world, getting gym badges, and inexplicably saving the world (and then beating the Elite Four). Your Pokemon can talk, and you even are a part of a guild with nothing but other Pokemon. You're even a silent protagonist that at least lets the player know his/her thoughts!

And the series is a rougelike. That turns off a lot of people, but it's a good kind of hard. Your first Monster House will very quickly teach you to be wary of any room full of treasure. And you'll quickly learn to be cautious too, since defeat takes a good chunk of your items away. Permanently. And whereas in the main game, stats are a big factor into how good a Pokemon is. This isn't entirely the case in PMD, ignoring the sought-after Kecleon who is a game-breaker. Evolution is locked at first and it's not as useful as it is in the main games. Your Charmander will get a whole +10 to all non-HP stats when evolved to a Charizard. Not terribly significant, and if, say, you befriended one and it joined your team, its stats could be well below your own teams' if you've been giving them the proper foods.

Yeah. Regular Pokemon is old and tired to me, sorry. Mystery Dungeon is a nice RPG spinoff that plays similarly to the core series, but not too similarly.

Also, Stantler.

I prefer it over the core series of games.

I've gotta go with Gold and Silver. They were the high point of the series and easily the most complete games to date (two regions, sixteen badges, day and night cycles). The original Red and Blue are an extremely close runner-up for me. The first two generations both hold very high place in my list of favorite games. The recent Heart Gold and Soul Silver also happen to be the most I've enjoyed the series since the GBC days.

Bonus: I can't choose just one.

Silver!!! Gold can shove it

BQ Wartortle

Gold/Silver

Silver's my favorite, even though I bought Gold for myself this generation. And my favorite critter is Metagross.

well... i vote for Pokémon Red/Blue. Original games, both kickass, and the first 150 pokemon are the best. although my favorite pokemon is Altaria though.

Gold/silver, 1st gen is the only one that comes close.

Favorite pokemon are cyndaquil and torterra

Anyone who didn't give up at ruby/saphire/emerald should say heart gold/soul silver, it had just about ALL the good things of the new system. ( fuck, sure IVs and EVs and natures are complicated, but oh so gratifying, plus if all you care about is beating some of your friends and the game you don't need to get into it) only think I'd say is misssing is some of pokegear apps (not the calculator, but the clocks were somewhat good) and pogfins making. The shakes u can make seem rather useless ( at least 1 pokemon evolved with it's beauty stat) pokeatlon is win, game world is win. Ekans is win. Fighting red is win. And mostly in the games, first time through you'll mostly get recognizible pokemans... None of that bibarel stuff that happened after.

My personal favorites are Ruby/Saph/Emerald.

The only thing I've learned from this thread is that the people answering are young. Anyone who thinks Gold/Silver were better than Red/Blue is seriously delusional. Screw how much content it had, the Gold/Silver Pokemon are lame as hell. The game world isn't very interesting until you unlock Kanto, and the starters are terrible.

I should be answering Red/Blue as the have the biggest influence and my best memories, but I'm going with what I've played most.

Bonus Question: Kyogre/Sharpedo