1) If you are just looking to wake from S3 sleep, then any USB IR remote will do. All recent motherboards allow you to wake from USB. If you get a case with a built-in IR sensor, it may have a 24-pin adapter that allows power on from a full off state. S3 is what you want however, so you don't necessarily need a case with the adapter.
2) No, you don't need a particular motherboard unless you plan to connect the IR to an internal CIR header. USB IR or case integrated IR is a much easier solution.
3) No, you don't need USB 3.0. USB 2.0 is perfectly fine for a USB IR receiver.