Too many to count, but screw it, I'm going to try anyway (and keep it to one entry per IP)
-Advance Wars: Days of Ruin (this has a mixed reputation, but it's my #2 AW game)
-Aliens: Colonial Marines (yes, I genuinely like this game. Even if it had a false advertising campaign, that doesn't mean the game itself is bad. Fuck, I like it more than Isolation, which had even more bugs)
-Call of Duty: Infinite Warfare (I get why the CoD fanbase dislikes it, but as someone indifferent to CoD, I really enjoyed it)
-Command & Conquer: Red Alert 3 (why do people dislike this game? It's my favourite RA game)
-Diablo III (I don't know if everyone dislikes it now, since the game was turned around pretty well, but it's actually my favourite Diablo game)
-Doom 3 (TBH, it's my favourite Doom game)
-Golden Sun: Dark Dawn (it's the weakest of the trilogy, but I still think it's a good game, just not as good as its predecessors)
-Halo 5: Guardians (yes, I like this game. Not perfect, but it's better than Halo 4, which people seem to like now for some reason)
-The Legend of Zelda: Spirit Tracks (this isn't my favourite LoZ game, or even my favourite 2D LoZ game, but out of all the ones I've played, it's the most underrated IMO)
-Metroid: Other M (there's plenty of valid criticisms of this game, but I'm much more generous to it than a lot of others - I rank it higher than Hunters or Metroid II at least)
-Resident Evil 5 (I don't think everyone "hates" this game, but most people regard 5 as the start of a shift towards action, even if that shift technically began as early as 3. Semantics aside, I like 5 more than most people, and it ranks fairly highly on my RE list)
-Sonic the Hedgehog 4 (treating this as a complete package ala STH3&K, then yes, I really like this game. Ep. 2 does a lot of the heavy lifting, but I had fun with this.)
-Star Fox Adventures (this game gets way too much hate. Yes, it's an atypical Star Fox game, but it's better than quite a few in the series...yes, I'm looking at you, Command!)