Uhh lets see how bout Washu from tenchi myuo >.< (shes the life of the party)

guys huh lets see uum Ah Hojo from Final Fantasy 7 (i hate him >.<)

uum Batman LOL hes a geek.. (but the best superhero ever!)

uhh Lelouch from code geass.. (ahh man but hes cute)

uuh *looks around room* Faust from shaman king... ah man thats all I got..... hope this helps! (eeww my sister likes him >.<)

@TimeChaser:

wow an outlaw star fan! WOOT WOOT!

I think that General Hughes fits this prescription..

Roy Mustang
Shigure Sohma
Reno
November 11
Rentarou Futaba
MakubeX
Ginji Amano
Haré
Sai Nanohana
Shinobu Morita
Hayate Ayasaki
Howl
Roy Mustang
Llyod Asplund
Sunohara Youhei
Yuuichi Aizawa
Jing
Keiichi Shimizu
Hosaka
Orphen
Usui Sadimitsu
Eiji Kikumaru
Louie
Touga Kiryuu
Shizuma Kusanagi
Kouyuu Li
Nozomu Itoshiki
Tamaki Suoh
Kamina
Micheal Lee
Makoto Kousaka
Death the Kid
Haré

Oh, and you want manga people, too~!? :OOOOOOO
Well then...
Soji Okita
Kenji Harima
Hideaki Asaba
Satoshi Shimonuki
Kazuya Hasukawa
Ga-Woon Kim
Ezawa

OK, so this is getting ridiculously long. > >;;

About the only one I can think of off the top of my head is Jim Hawking from Outlaw Star, since he's the show's resident computer geek.

This one is more of a boy, but hes cool.

Tsuyoshi from Kodacha

Define geeky (I'll go with my favorite smart bishies XD) and picture links credited to Wikipedia XD Actually, I'll just link the whole page.

Kurama from YuYu Hakusho {wiki took off the pic -_-}
Uryuu Ishida from Bleach
Guy Cecil from Tales of the Abyss hmm...going by Wiki is seeming to fail me for pics {Guy goes geeky when there are machines around XD}
Kyouya Ootori from Ouran Host Club pic
Hatori Sohma from Fruits Basket pic
Bulma from DBZ
...and then I could go on with non-anime characters like Brooklyn from Gargoyles and Brite Heart Racoon from Care Bears, Malory from the Mighty Ducks Cartoon, Gadget from Rescue Rangers... {etc etc etc}

{I didn't know if you meant 'guys' as in males or as in people in general, so I included a few girls XD}

hmmm. I'll think of some and come back to edit this comment. lol.
:D
~Wall-iE
edit-
There Alvin from the manga "last hope". He's a genius!
And yamazaki from card captor sakura... pretends to be a know it all.
.... well, I think shishou mentioned the rest XD

Yes, Keitaro from Love Hina is pretty well the greatest example of that type of character.

Others? Hmmmmm...

Ah, the guy from DNAngel! Not Daisuke or Dark, but the blue-haired kid with glasses that turns into Krad!
*goes to Google*
Satoshi Hiwatari!

How about Kain Furey from Fullmetal Alchemist?