Link, Cloud and Naruto are right out. Zelda is close enough with SSBM. They are far too overused in the gender-swapping fan-art fandom...

Here's a few off the top of my head (to change the gender of)

Derek Stiles (Trauma Center) - he's practically a magical girl already
Bowser - Nurse Bowsie for Dr. Mario! (Seriously, a friend has drawn that on my suggestion as fan-art)
King of All Cosmos - (Katamari Damacy) or maybe not *imagines* *shudder*
Lucca - (Chrono Trigger) - And for that matter Robo in a humanoid form would be cool!
Everyone in Earthbound - a straight swap of everyone's gender.
Shredder...
The Tales of Series always has some that need it - Zelos, the entire cast of Abyss (even Mieu).
Princess Daisy - or at the very least she needs her own brawler or something and the chance to really unleash hell like the boys. The sports versions have been a good start.
Aeris - quid pro quo. Cloud has been changed so many times that their pairing is nearly girl-girl X_X
Mother Brain - or at least turn into a humanoid.

Also, I know he's a sexist vampire, but Demitri's Midnight Bliss would rock if it went both ways (rather than just making girls or girlier girls).
On side note, I love how Plenair is sort of the transmigrated avatar of the main artist (Takehito Harada) for Nippon Ichi's games.


Edit - Examples of what I am talking about

http://fc03.deviantart.com/images3/i/2004/163/3/e/Lady_Link.png - Link
http://fc01.deviantart.com/fs16/f/2007/182/6/7/FF7_Gender_Bender_Extravaganza_by_Shiankra.jpg - Final Fantasy 7