I don't know if anyone's mention this before, but I happened to run into the fantastic-looking Compatible Amiga Programming guide:
http://guidetoamigacompatibleprogramming.googlecode.com/svn/trunk/english/

I hadn't heard of it before, so maybe it's new-ish, or maybe it's old & abandoned, I don't know. But from a cursory glance it looks like a great introduction to programming Amiga-like computers.