GameStop pre-orders for Xbox 360 and PS3 will get you a code to unlock Sideswipe, while Amazon pre-orders get you Ratchet (and a $10 credit). But the Wii and DS games, pre-ordered anywhere, get you actual toys -- Bumblebee with the Autobots game, and Lockdown with the Decepticons version.
Other bonuses announced by Activision include an in-game Bumblebee skin for the 3DS version at Toys R Us, in-game "Deco" character skins for the Wii and DS games at Target, and a, "original, limited edition Transformers: Dark of the Moon comic book" at Kmart and Sears, seemingly not tied to any particular version.
Or you could pre-order from Best Buy and get a "free movie ticket upgrade to 3D." Thrilling.