I have been using Auto Trim with my APM 2.5 for quite some time. Just recently I decided to compare Auto Trim and Save trim to see which one can provide greater stability. This video walks you through the process of setting both methods up and compares them.
I must say that Auto Trim is much easier to configure since it pretty much works after you get your ArduCopter configured for flight. Save Trim takes a fair amount of work to setup as you'll see in the video. Both provide great stability, but I'd have to say that I feel like you can get greater accuracy with the Save Trim approach.
I think I'll continue to use both methods, but Save Trim is the way I'll go when I want to get my ArduCopter locked in. This test was run with ArduCopter 3.0.1 firmware.