I've played countless hours of RTCW and RTCWET and punkbuster is a godsend. Its totally seamless; the only issues I have seen is on a low-spec machine, with all the bells and whistles off, some servers complain via pb that my configuration is not accepted. (Turning off the dynamic lights, shadows, etc can really give you the advantage spotting the enemy at distance, so I consider this the admins prerogative.) This was not modifying the config file, btw, only setting things via the ingame menu.
Otherwise, check out rtcwet, and you'll find very few, if any, cheats. PB scans the game exe as you play, so a modified exe (with wallhack, for instance) will get booted. I believe, also, that id and nerve agreed that anyone caught with a modified exe would be banned, forever, from the game, ie have the cdkey destroyed from the auth server. Thats what I call taking cheaters seriously.
On a side note, I've been playing bf1942 demo, and like a lot of what I see, but on the ground infantry seems way underpowered. I'm having a hard time getting kills at even moderate distances, where in rtcw I can dominate a public server on a good day. This is a real turnoff; vehicles are great, but accuracy and smart tactics with a rifle need to pay off too.
Has the weak infantry weapons been addressed in any of the patches? I'm really seriously considering bf1942, but if I get fragged one more time by some retard engineer with a satchel charge, after loading him full of lead from 25 meters, I'm going to give up on bf1942.