Here's the exclusives for the game's VIP site.
http://web.sm3thegame.com/indexnew.php
Stuff in every version of the game
* Large, open ended world (most likely excludes GBA).
* 10 different storylines (possibly excludes DS and GBA, two of the storylines are different on Wii, PS2, and PSP).
* Symbiote Suit's Rage System (excludes DS and possibly GBA).
* Movie storyline (possibly modified one for GBA).
* When the game is 100% completed, there is a secret unlockable (unknown if also for Wii, PS2, PSP, DS, GBA versions).
Wii
* Unique controls featuring the Nunchuk and Wii Remote.
* Mobius and Shriek as bonus villains (confirmed here)
* Ability to switch between the symbiote suit and traditional suit at will.
* Excessive use of the symbiote suit and high crime rate will effect the city (dark and moody clouds, trash build-up, grumpy citizens, etc).
* Pressing the C button will re-center the camera behind Spider-Man.
* Holding the C button and moving the Nunchuk horizontally or vertically will allow you to look around freely.
* Cineractives will use motion-controls.
* Cineractives will take place in different places than the 360/PS3 version.
* Supports 16:9 and progressive scan.
* Will have unique unlockables not on 360 or PS3.
360
* Functionality with Xbox Live (not multiplayer).
PS3
* Has a Collector's Edition that has an extra DVD with special content. The DVD contains webisodes from the SM3 movie, interview with Avi Arad, behind the scenes talks with the cast of SM3, special SM3 trailers, and more.
* New Goblin is playable in the Collector's Edition version.
* New Goblin is controlled by the SIXAXIS gamepad.
* The SIXAXIS is only used by NG and the Cineractives. It is not usable during any other gameplay.
* As New Goblin, you can play in 10 exclusive missions and participate in Crime Events.
PS2
* Has a Collector's Edition that has an extra DVD with special content. The DVD contains webisodes from the SM3 movie, interview with Avi Arad, behind the scenes talks with the cast of SM3, special SM3 trailers, and more.
* Morbius and Shriek as bonus villains (confirmed here)
* Ability to switch between the symbiote suit and traditional suit at will.
* Excessive use of the symbiote suit and high crime rate will effect the city (dark and moody clouds, trash build-up, grumpy citizens, etc).
* Controls are more like the PSP version.
* City is 2.5 times bigger than SM2 for PS2.
* Cineractives will take place in different places than the 360/PS3 version.
* Will have unique unlockables not on 360 or PS3.
DS
* Full touch-screen fights and web swinging.
* Unique missions (different than Wii and PS2).
* Open ended word is only a little smaller than Wii's and PS2's.
* When angered, the symbiote costume takes over and you're able to use your abilities immediately.
* Ability to switch between the symbiote suit and traditional suit at will.
* There will be a DS Download Demo of Spider-Man 3 for the DS sometime around May. -NEW-
PSP
* Morbius and Shriek as bonus villains (confirmed here)
* Ability to switch between the symbiote suit and traditional suit at will.
* Excessive use of the symbiote suit and high crime rate will effect the city (dark and moody clouds, trash build-up, grumpy citizens, etc).
* Cineractives will take place in different places than the 360/PS3 version.
* Will have unique unlockables not on 360 or PS3.
GBA
* Ability to switch between the symbiote suit and traditional suit at will.
PC
* Same version as the 360, ported by Beenox.