For straight PDF reading, have you thought about Evince? It works very similar to FBReader, in that it doesn't exactly do bookmarks, however it will remember where you left off and re-open the file at that point.
Personally, I use the Calibre/FBReader/Evince combination with pretty good results. I do try to convert everything to epub, though. But I also realize it's not always possible, or even desirable to do so with some PDFs.