Heh, yeah. Completely forgot how it was spelled, so just wrote something remotely similar.

Guybrush Threepwood and Murray!

April Ryan and Crow.

Prompted by Wishbone:
Wizball and Catellite

Must be a trio right?
Yup well go with that :D
Sexist :o
And they constantly fight and discuss things, clank says "i dont think thats a good idea" ratchet say "Coooooome ooon" and they go on and on and on...

Am I the only one who is convinced that this thread is about Gabriel Knight and Grace Nakimura?

HAY GUYS WAT ABT. MASTEAR CHIEF I MEAN THATS NOT A DUO BUT STILL LOL WEL MABE WITH CLOUDSTRIF plzzzz SQUARESOFT!!!!!!!!!

No, the boobies form their own seperate but connected entity and therefore count as a single unit. When sad pathetic teenagers were whacking off to early renders of Lara (I was 21 at the time so its not sad & pathetic when I did it), were they looking at just one or looking at them as a unified whole? I think that almost everyone was doing the latter (or wishing they could do them anyway) and because of that,
Sexist :o
it was the objective of 1 & 2 to rescue her, 3 to cure her of the curse and she's at the whole bondage on a ship thing again in Tales, I think she likes it. She was the objective making her an object (especially in 3 where she basically became an object). There, I've objectified women!

Well master chief and cortana could count but they're nothing special really, badass space marine ripoff and sassy female voice in your ear, big whoop.
if you're going for badass and sassy voice in the ear, I'd pick Sam Fisher & Anna Grimsdottir from Splinter Cell

I think I'll have to go with Max Payne and Mona Sax on this one.

i totally forgot morgan freeman and alyx
okay not in the first half life 2 but certainly in the following episodes

Okay, I'm not a Half-Life fan, but if they made a movie and cast Morgan Freeman as Gordon Freeman, I would watch the shit out of it.

Great , finally someone notices :)
it took about 2hours untill someone noticed that it should be GORDON :D
you've won the eternal fame of duo knowledge.

I pretty much agree with everything else said in this thread, but I would add:
Gage Blackwood and Arthur from The Journeyman Project 2 & 3. Okay, never mind Gage, just give me Arthur, any day. Nothing like a artificial life-form companion that doubles as a resident encyclopaedia of world history, and stand-up comedian to boot. ;)
And if I'm allowed to slip in a trio, I would also add Hernie, Bernie and Hogie from Day of the Tentacle.
Late edit:
Fixed a typo.

Has to be Ryu and Ken from Street Fighter for me.