We used the proficiency systems (weapon and non-weapon), individual initiative, complete handbooks, parrying, jogging and running rules, we added a new stat for Perception, and we tried out the subabilities for stats in PO: Skills and Powers (boy, was that a mistake).
I also fiddled with house rules on crits/fumbles, saving throws (particularly ones where the thief didn't suck so badly), and energy draining that presaged some of the ways 3e would ultimately modify it.