DOOM 3; not the most hated game ever, but one that has certainly been maligned by many gamers for a few perceived flaws, namely; it's too dark, the scares are cheap and "monster cupboards." The latter two criticism are valid, but, imo don't affect the gameplay, but I disagree about the former. I think the darkness really adds to the atmosphere. DOOM 3 is one of my favorite games to replay.
Bioshock 2; Bioshock 2 may not live up to the greatness of the original but it is a very good game in it's own right. There are enough familiar aspects from the first game but there are also new elements that make it it's own entity. Being a slow, lumbering Big Daddy and using the little sisters to gather adam for you while you fight off hordes of splicers makes for a tense experience.
Heretic: Shadow of the Serpent Riders; Heretic is usually only known for being the prequel to HeXen and is often disregarded as the black sheep of the DOOM engine, or id Tech 1, games. Heretic is my favorite DOOM engine game, however. The game world and sprites are bright and colorful, the gameplay is crisp, though possibly a bit too easy, and the maps are well conceived.