Mass Update:
48. Age of Empires III (& Expansions) (PC)
Third game in the Age of Empires series of RTS games (fourth if you include Age of Mythology). This one added some new gameplay ideas such as adding mecenaries, fixed trade routes and a levelling home city. Some of these ideas can be seen in the recently released Age of Empires Online.
47. Tekken 5/Dark Ressurection (PS2/PSP, also on PSN)
One of only 2 beat-em-up on my list. I could never get on with the 2D fighters (partly because I sucked... well, mostly). In Tekken, everything just seemed to click and this represents one of the best in the series. I haven't got 6 mind and the new Street Fighter/Tekken games looks to have potential...
46. Prince of Persia (PS3, also on 360 & PC)
I've always felt this game got an undeservedly hard time. Yes, it's not as hard as the previous games, the enemies are a bit dull and fights a bit repetitive, but platforming mechanics were just a joy that few games can replicate. The sheer perfection in the platforming mechanics combined with the impressive art and intriguing characters are what made this game great.
45. Duke Nukem 3D (PC, also on iPhone, Xbox Live and N64)
Going down my list I think this is the only 2D shooter. At a time when FPS' were taking themselves too seriously, along came Duke, his babes and 80's one liners. Beyond that though the guns were fun, levels huge/inventive and boss battles epic. Really should have stayed in the 90s though.
44. Tomb Raider Legend (PC, also on PS2, Xbox, PSN, XBL, and in the HD Trilogy)
In the last gen, Tomb Raider and Lara Croft needed a makeover (like this gen actually). They got it in spectacular form in Tomb Raider Legend. The mechanics were vastly improved so they were more in-line with Prince of Persia, but it kept the puzzles and Indiana Jones-esque feelings of adventure.
43. Age of Empires: Online (PC)
The new free-to-play Age of Empires game takes some of the best aspects of the series and places into an online environment. The basic AoE gameplay is still there but with more customisation, odd cartoony graphics (that somehow work) and an RPG-like levelling system.
42. Final Fantasy X (PS2)
This felt a bit linear for a FF game but the story and new strategic battle system kept me plugging through the game and I'm glad I did. The graphics at the time were pretty good too.
41. Bomb Jack (Amstrad CPC 464, also in Arcade, also on Commodore 64/16, Atari ST, Amiga, Game Boy and now on Wii Virtual Console)
This is the only video game my mother has ever played. Younger posters are probably thinking 'WTF?' but this game is pure platforming brilliance. Someone has planted 24 bombs in 5 high profile locations and it's up to Bomb Jack (with his impressive jumping and gliding ability) to collect and defuse them. Collect the bombs in the right order (denoted by the order the bombs sparkle) and get a massive bonus. But watch out for those fast moving robots! Now on Wii's Virtual Console if anyone wants to give it a go.
40. Neverwinter Nights 2 (+ Mask of the Betrayer & Storm of Zehir) (PC)
This game modernised Neverwinter Nights to some extent whilst still retaining much of what made Neverwinter great. A solid RPG with some interesting characters if a little stereotypical. Was also nice that you could control multiple characters in your party rather than just having a single henchman. Mask of the Betrayer added extra story whilst Storm of Zehir added some old school adventure seperate from the rest of the game.
39. Unreal Tournament (PC, also on DC and PS2)
This game was a revolution; the first game marketed as a pure online shooter. Fast paced action, multiple game modes, superb level design and a plethora of weaponry made this game sublime. Unreal Engine and Epic would never have been so big if it hadn't been for this game's success.
38. Tekken 3 (PS1)
Perfected the fighing mechanics in Tekken 1 & 2, mechanics that haven't changed a whole lot since. All the Tekken games since have replicated the mechanics of Tekken 3 only adding small evolutions to a brilliant game.
37. Assassins Creed II (PS3, also on 360 & PC)
The first game was a bit boring and repetitive. The sequel completely changed that with a massive playable world but with interesting quests and just generally filling the game with some superb content.
36. Age of Mythology & Titans Expansion (PC)
Brilliant Age of Empires gameplay combined with creatures of myth/legend and powers given by the gods. Was also the first 'Age of' game to go 3D. It worked and I still enjoying playing 2-player with my girlfriend.