Mentalepsy: I can't think of any games that I like that were totally hammered by reviewers, because truly terrible reviews are somewhat rare unless the game is fundamentally broken.
But, two that come to mind that weren't particularly well-received by critics are King's Field: The Ancient City (Metacritic 60) and Bloodrayne (Metacritic 65). King's Field is a niche series that reviewers never seem to "get," and Bloodrayne is simplistic, but wildly entertaining - one of my favorite turn-your-brain-off bloodbaths (I'd call it a guilty pleasure, except that I don't feel guilty in the slightest).
Thunderscape was largely ignored at release, and I think reviews of it were lukewarm at best, but I adore that game. I wish Ubisoft would stop sitting on it and let GOG have it.

Arteveld: And then there's The Detective Game for the C64, which generally got some bad reviews, ZZap somehow gave it a 78%, which is still too low.

El_Caz: Mount and blade got a 72 or something like that on metacritic and it's probably one of the lowest score games I have on my Steam catalog... and it's the one I've played the most WITHOUT any mods even.
Storyless, dated graphics, pretty much a combat simulator more than anything and it sunk many, many hours of my time. I can't say it was a "bad game" at all, but many players expect something else from it (like a plot and getting told what to do) and they get disappointed while others like it because of the mods mostly, but I thoroughly enjoyed the vanilla version until all the villages and cities were under my banner.
After I enjoyed it this much, I stopped taking reviews to heart and now base my decisions not just on reviews but also on player's opinions, demos and some other factors.

Bodkin: Oh, and Daikatana of course. It, was good.

Arteveld: If I only had one.. I'll wait for a PC version, till then i'll replay the C64 one.

SLP2000: There are free DS emulators, you know ;)

jungletoad: Shinobi (PS2)- 71
The Red Star (PS2)- 72
God Hand (PS2)- 73
I find those last three particularly upsetting. They are three of the best action games on the PS2 and all 3 of them retain an old-school arcade feel. Some people think they got panned unfairly by critics for being too difficult.