Well, there's a whole new keyboard attachment (which you can play on guitar), so there's a new instrument.  there's pro guitar (you have to buy a special guitar to play it, but it actually teaches you real guitar), drums are upgraded, and if you got a rock band 2 drumkit it becomes a full 7-piece drumkit, and TONNES of new DLC, including this gem:  http://www.youtube.com/watch?v=fndzbtAhEWc

Not to mention the RBN, where normal folks can upload songs for people to buy.  Lots of advancements since the original. 

#40 Baldurs gate dark alliance played on PS2, released 2001

This is how you do spin offs. A great action RPG that is awesome to play onscreen couch co-op. The interface was perfectly tuned for the game, something that seems to be an afterthought nowadays.
The game was technically impressive too, rendering at double resolution internally and scaling it down to get FSAA. The real time rendering of ripples in water was a first in games and fun to play with on its own.
The gameplay is engrossing from beginning to end. The best co-op experience for me last gen. Dark alliance 2 was excellent too, as well as as well as Champions of Norrath, a spin-off of Everquest.
There are a few of these games available this gen as well but none of them get onscreen co-op right quite as well as these did.

List

40. Alan Wake (X360)

This game really surprised me. Sure, it has its' flaws here and there, but the overall experience is just great.

Hey, really sorry for not posting yet. For the last fortnight or so, I've had a fuckload of university assignments and reading to do, so I haven't had much free time (and what free time I've had was spent finishing Xenoblade Chronicles before Zelda came out).

I've just compiled my top 50, I'll leave it a couple of hours and come back to it and check through it again, possibly revising it. Expect me to start my countdown within the next 48 hours.

40. Banjo-Tooie (N64)

This is the second Rare game from their golden era on my list, and it won't be the last. After defeating Gruntilda in the first game and leaving her buried under a boulder, her two sisters arrive to dig her up and set about gaining revenge. My memories of this game are a little hazy given it's been a decade since I last played it, but I can remember enough to know that I loved it at the time. I wouldn't go quite as far as those crazy types that rank this game and its predecessor above Mario 64 though.

I have updated my list in the time between Skyward Sword playthroughs.

42 - PC - Grand theft Auto Vice City (Rockstar)
41 - GC - Eternal Darkness: Sanity's Requiem (Nintendo)
40 - Wii - SSX: Blur (EA Sports)

Nice choices everyone, Banjo Tooie was fantastic, but I didn't get to my best 50. I really want to try Alan Wake but i don't have an Xbox, I heard mixed thing from that game but anyway seems really interesting.

I updated my choices:

#43: Katamary Damacy Series(PS2): What can I say about these games? They are incredible fun and bizarre. Charming characters, great soundtrack and that feeling of power when suddenly you are the same size as a Giant Octopus

#42: Megaman X - X-4(Snes/PSX): When I was a kid, I loved Megaman with all my heart, the Megaman X series were a blast and I spent a lot of time getting the capsules of Dr.Light and killing every maverick on the game. Weird case is, I never beat any of them but X4, but even considering that, those games are the best of the megaman series.Period

#41: Zombies ate my neighbours(SNES) (probably a Typo on the name) : Local Co-Op? Monsters from B-Movies? Funny Pre-Level statements? Count me in!.

Man, to anyone who didn't played the game, i recommend to start playing right now. It's one of the best SNES game, altough it's VERY hard and kind of frustrating, it has a lot of charm and cool gameplay mechanics.

#40: Clock Tower (SNES): While some may argue this game is not the first survival horror, nobody would argue this game is effin scary. There is something on being a little helpless girld being chased by psychopaths and having multiple (and bad) endings. This game is a true jewel for survival horror fans.

40 - Shadow of the Colossus

Summary of the whole game.

"Hover-Tanks, Turrets, points, crying, beautiful!"

:D

Nostalgia does sort of kill things with this, doesn't it? I know the Pokemon games on my list are almost exactly in opposite order against how good they are objectively (except that Gold and Silver are ahead of RBY)