When I'm typing or playing TF2, more often than not I will have some keyboard and mouse delay. I originally thought it was just an issue with TF2, but then it started happening to me while I was typing. Also, sometimes I might get beeps while my keyboard and mouse freeze up, imitating my key presses in delay between beeps.
My motherboard is an Asus M5A LE R2.0, my processor is an AMD FX 4300, and I'm pretty sure this isn't just a USB issue. The PS/2 has this problem, at least for keyboards, and I temporarily fixed this problem by moving my mouse and keyboard to USB 3.0 and reinstalling the drivers, but it's started to have issues again.
It's very likely that this has to do with me getting a semi-faulty motherboard (onboard LAN doesn't work, have to use a card), but the peripheral lag has only started within the past two months.