Ok. Now that this is good and dead, and my exams are almost over, I've gotten around to doing some tallying, and only tallying (no weightings by preference, just mentions). It's taken about 3 hours for the first page. More if you include writing a program to help. So I should have some results for you soon enough.
Notes: Mentions of Pokemon have been lumped by generation. i.e. if you said Pokemon Gold, it counted as a mention of Gold, Silver and Crystal. If you mentioned a series, I have tallied that seperately and will decide what to do with it at the end, but if you have then specified your preference in the series, I have used the individual votes instead. Also, chaos_aquarium, swell chap that they probably are, managed to get me off guard with a list of 30. At the end I will decide whether to go back and subtract the last 10 votes, or keep the list as is, probably depending on how hotly contested the games are.
So far, Fallout 3, Skyrim, Portal, Portal 2, Ocarina of Time, Fallout: New Vegas, Mass Effect 2 and Windwaker are winning, with above 6 mentions each.
UPDATE: After 2 pages including the first, here are all games with 10 or more mentions: Mass Effect (13), Mass Effect 2 (19), Mass Effect 3 (10), Okami (10), Windwaker (14), Bioshock (11), Final Fantasy X (11), Fallout: New Vegas (18), Ocarina of Time (14), Portal (21), Half-Life 2 (13), Portal 2 (16), Pokemon Gold/Silver/Crystal (12), Dark Souls (12), The Walking Dead (11), Skyrim (19), Journey (11), Shadow of the Colossus (13), Resident Evil 4 (12), and Fallout 3 (18).
As you can see, Portal is winning, with New Vegas, Fallout 3 and Skyrim close behind. You may be interested to learn that by this point, about 565 unique games have been mentioned. Which means I have personally typed out and then made an acronym for each one. I may lose motivation in the near future. If that occurs, consider Portal the Escapist's favourite game. Until the next update.