I find there is no difference in performance with internal (PCIe) tuners or external (USB and Ethernet). I have mixtures of both on various machines. I've had no trouble recording HD from six external tuners all at once via Ethernet using SiliconDust tuners.
The only external USB tuner that's worth a damn is the Hauppauge 1950 in my experience. I'm guessing the Ceton USB quad cableCARD tuner works well too. Hauppauge also has a USB dual cableCARD tuner, though I have no experience with it either.
I did once have a Hauppauge USB tuner that lost its analog side - the QAM still worked, as well as the IR remote receiver.