Yes, Apple Remote (aluminum or plastic) should work well since the IR sensor is on the front of the machine next to the power indicator led. I'm unsure about aftermarket ones.
I went with an Apple plastic one as it was $5 as opposed to $25 for the aluminum one.
Yes the apple remote works fine. I use an old white plastic one that came with our now defunct white iMac - works well. Also the remote will pause, play, fast forward etc.
On a separate note, I picked up a USB dongle called FLIR and it adds functionality of an IR sensor to my Mini. They stopped adding the IR sensors to Macs in 2013 I believe.