Denny Atkin's Best Amiga Tips and Secrets still sees a lot of use around here. And the manual to ImageFX is also rather dog eared...
Yes, Denny wrote a great reference.
Rob Peck wrote an excellent guide to the Amiga's OS in "The Amiga Companion"
I still use both of these from time to time.
If you're into hardware, Sam's Photofax on the A500 has a great deal of info beyond just a schematic.
