What's wrong with Calibre? Works fine for me. Sure the UI is a little much, but once you figure out a routine, it just works. It could be better, but right now it does pretty much anything I could want to do with eBooks.

And, sorry, I think your argument about legal | not legal is bunk. If someone has bought an eBook, they help themselves to a pirated copy -- in some ways, that's best of both worlds. It would be quite nice if one could just buy a non-DRM from the get-go, but whatever.