Metal Gear Solid: Peace Walker/WMG

Huey founded Aperture Science

Huey apparently had a hand in designing all the unmanned AI weapons; the Pupa, Cocoon, etc. They all sing that song when they move about, and announce their attacks in a sing-song synthesized voice. Clearly, Huey and Aperture Science have to have some connnection. (Other than Kojima Prods. ripping off Valve/Portalteam wholesale, natch.)

Kaz really was working Cipher(The Patriots)

Both he and Paz were double agents in getting to Big Boss, and his confession was a back up plan just in case Paz failed. After learning everything he can, eventually turns on Big Boss in Metal Gear and help Solid Snake into taking him down.

Post Game Paz has Amnesia

To think some of the things that happen in this game are non cannon would be ignoring all the other blatant 4th wall breaking stuff MGS has taken into the fold of it's chronology before (unlimited ammo anybody?) so the stuff you do with Paz post game either take place before the final battle, or because she survived the drop and just suffered some amnesia. Or she could be faking it and everyone is choosing to believe she forgot for decencies sake. After all, no one really bothers to talk about what happened that much, considering what a big deal it was, so maybe they're keeping it all bottled up, or going with the ignorance is bliss route.

Chico grows up to be one of the bosses Snake faces off against in the original Metal Gear.

Dr Strangelove is not Otacon's mother.

Rather she is his stepmother (ie. E.E.'s mother) with whom he had an affair. She's mentioned as being English in MGS 2.