My "favorite PC game" from a quantitative standpoint (that is, most hours dedicated to it) is Skyrim. Over the past nearly ten years, I think I've spent a cumulative two months of my life playing it. (~1500 hours) It's ridiculous.
HOWEVER. My "favorite PC game" from a qualitative, personal preference/fondness standpoint, is Fallouts 1 & 2. I realize those are technically two separate games, but they blur together in my mind to where I rarely think of one without thinking of the other. I loved everything* about those two games, from the S.P.E.C.I.A.L. system to the humor and random references, to the ambience and premise. None of the Bethesda era Fallout games (except to some degree New Vegas) have really recaptured that same style or tone, in my opinion. (Sadly neither did Wasteland 2.) I know they're not the best games by any stretch, but they'll always hold a special place in my nerdy core/brain/heart.
(* - okay, so I didn't love it when Marcus would mow down a fellow NPC because they got in the path of his minigun.)