I certainly disagree on Skyrim at #1, but the way PC Gamer does its Top 100s is quite unconventional (at least in the UK mag, in all previous years). The basis for entry is just what they have actually liked playing over the last 12 months, rather than a very academic discussion about HL1's contribution to the FPS genre or whatever. TF2 came in at first once, because they had been playing that all the time that year. There's an Italitan-themed football manager game from the late nineties that gets in most years, because Graham Smith, the UK version editor, became absolutely obsessed with it at the time and it still means a lot to him personally.
Even with the very informal ranking system, it really sounds bizarre having a game as dull as Skyrim at first place.