the combat maneuver bonus/defense were significant changes, but mostly for me, its about the level 0 spells, cleric/druid domains, and magic item crafting. in PF, you can cast lvl 0 spells an unlimited amount of times per day, and magic item creation has no XP cost, where in 3.5, it costs xp. In 3.5, druids couldn't choose a domain of fire, water, earth, or air, and were forced to have animal companions ( which also function slightly different), and cleric domains in PF include a basic spell castable 3+wis modifier number of times per day.
In my tabletop PF campaign right now, i have a druid of the fire domain and no animal companion, with a number of item creation feats, thus the 3.5/PF differences hit me several times.