perhaps these three games weren't hated, just extremely under appreciated:
no one lives forever (PC)
no, not the console port. this was a pc game first and they bungled it when they ported it to the consoles. but the game is brilliant. do what you can to find a copy (the first one, not the sequal) b/c it's truly one of the most enjoyable times i've ever had with a game. the levels are fantasticly original: free fall from a crashing plane with no parachute while having a mid air gun battle with enemy sky divers all while trying to catch up to a guy falling below you so you can steal his parachute and land safely, infiltrate a top secret tropical facility, board a rocket, and go to an even more top secret space station, track down an antidote for a evil terrorist plot which involved turning humans into biological time bombs, and escape as a meteor shower is destroying the station, board a tanker ship looking for evidence, escape as it gets blown up and sinks, and then return to the sunken ship in the next level and scuba dive into it to finish the job, all while battling sharks and enemy scuba divers with a spear gun. and those are only a few of the many levels. oh, and the game is set in the 70s spy era and is very james bond-ish as well as freaking hilarious (the funniest games i've played). it's truly brilliant
mafia (PC)
again, not the shody console port. a 30s era GTA, this game has a great story and terrific levels which are probably the most well balanced levels of any game i've played. i finished nearly all of them with only a couple bullets and practically zero health, the sign of excellent design. sadly almost no one played it.
Arcanum (PC)
possibly my favorite rpg. set in a very cool world where magic once held sway but is being pushed aside by an industrial revolution, this is a game with depth, a great story, racial tensions, and the highest level of replayability and character customization i've ever seen. the number of ways you can design your character are staggering and you can essentially play vastly different characters, and thus have vastly different experiences, every time you start a new game. you can be an eloquent bomb making herbalist, a smooth shotgun toting pickpocket, a deformed fire ball flinging genius, or anything in between. sadly the developer went out of buisness but this game is well worth tracking down for fans of the genre.