Well, here's my personal list:
Chell's Mind by CyhAnide, The Point Man's Mind by Triox45, Stark's Mind by Anion, Freeman's (-ish) Mind 2 by Centaur1um, Mind of Ryan by DravenMario, and possibly Shephard's Mind by Krimsin if you can ignore some of the dated jokes and uneven characterisation. Kane's Mind gets an honourable mention if only for the fact that it's still being made and the guy deserves brownie points for sticking to it, and if you're an absolute completionist and don't have too high standards then I guess Barney's Mind does too.
EDIT: I removed Taggart's Journey by Blue15bomber from the list after he got complacent and stopped putting effort into his episodes. It hurt to do it because that series had so much potential, but I guess that's what happens when you let the pressure get to you.