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They are the same height, HOWEVER the PS2 dualshock 2 controller is taller than the PS3 sixaxis one, giving the illusion that the ps2 controller's stick are taller.

Here's a pic for comparison:

PS2 controller on the left, PS3 on the right.
There might be some differences on the the controllers, but the only ones that are really noticable by the feel, are the R2 and L2 buttons on the D3 ( I find these better on the D2), and of course the D3 is cordless...
4zb41, thanks! i have used a ps3 controller before and i thought the thumbstick felt longer, but i wasn't sure.

the reason i wanted to know is because i've put PS2 thumbsticks in an xbox controller before, and they felt really short. i was contemplating buying some PS3 thumb sticks, but didn't know if i'd get the same result or not.