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K2 for "regular" reading w/notes exportable to K4Mac, B&N's NookStudy or B&N eReader for academic stuff.
The latter because it's easier to search/flip through to find a particular passage, and they've got different styles of markup/highlight colours to use, which can be annotated with tags and such and viewed in a handy index.
Also I can copy/paste passages with citation information, and in the B&N eReader version, export all notes and highlights at once and have them shareable if I send along the .kz or whatever it is file that's generated when a book gets marked up (NookStudy only exports notes; highlights must be copy-pasted, and everything is only backed up to your personal account, no sharing.)
As for K4Mac and the Kindle device, as of firmware 2.5 they no longer use quite the same type of .mbp file, so while you can drag your .mbp files for a non-Amazon book from a Kindle device to a K4Mac and have it work with the book and show all your notes and highlights, it doesn't work the other way around unless they've changed things as of K4Mac 1.4.
But you're using an iPad, so the point may be moot.
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