Vehicle control is a bit better on PS3, though the view auto-centers, making it a pain trying to view the map while keeping an eye on the road. Steering vehicles with an analog stick is better than using the keyboard, though aiming turrets and virtually every other weapon is superior on PC with a mouse. Also, the sensitivity of the PS3 analog doesn't ramp up gradually; there's a sudden increase in turning and aiming speed as you tilt the stick further that takes more getting used to than in competing titles. It can also be difficult to control sprinting on PS3, since it is triggered with L3 (clicking the left stick), and will suddenly drop off if you try strafing while running.
You could get PC-like precision if they'd let you change the button configuration — something the PC version lets you customize entirely. Well, with one caveat. If you remap the use/interact key from default (E, Triangle on PS3), sometimes you'll still have to use E to dismount turrets or get out the back of a vehicle, no matter what you mapped the function to (it also forces you to toggle grenade types whenever you hit it). There is no way that I've found to fix this (if you know — besides mapping it back to E, smartypants — let me know in comments), though the problem doesn't happen on consoles...perhaps because you can't remap the controls. Hrmph.
Yet another important difference stems from the PC allowing you to save your game literally anywhere, any time, whereas the PS3 version only allows saving at safe houses and other predefined areas. It's not clear why this is different, and I played on the same difficulty level in both, so it's not related to that. Some prefer the challenge of having limited checkpoints, but I would err on the side of save-anywhere functionality and then simply not use if it you so choose. In this regard, PC wins.
Furthermore, in my experience saving your game on the PC is nearly instantaneous, while on the PS3 it takes a few seconds. Save files on both keep a thumbnail screenshot of where you were when you saved, but in the PS3 you're usually facing the save box on the wall in a safe house (except during mandatory checkpoint saves during missions), which isn't terribly helpful. The PC's free form save system opens you up to save when facing a particular landmark, making it easier to recall where you were when you last recorded your progress.