The PC version of BF3 automatically installs Punkbuster by default, so you should be fairly safe from hackers there.
Biggest thing I've found from online play (mostly from SWAT4 & Halo:CE) is to find a clan server. I don't mean join the clan, just look for clans that run multipler servers. AshClan, P0Q & BFM are major server providers in Halo:CE, for example. Their servers are open to both clan & non-clan players, but the clan members are good about keeping an eye out for potential hackers... & they don't just auto-ban/perma-ban you because someone whines & claims that you're aimbotting them, the server mod lets them see what's on your screen so they can determine if you're aimbotting/wall-hacking or not. They're also really big on players following the server rules (i.e. on a Halo:CE "race" server, your focus is supposed to be on getting a 'Hog & trying to complete laps, not on treating it like a "slayer" game).