Bookman is very basic, but does its job of creating the thumbnails and letting you do side-by-side pages when holding in landscape mode.
iAnnotate pdf software from Aji posted a positive comment about getting feedback and implementing. We'll see who can do the best implementation while keeping things easy to use with all the features people need.
So far, I really like the iAnnotate for its functionality of adding notes to a PDF, but GoodReader has a lot of sharing importing and viewing of other file types down really well.
The other readers I've seen have one or two aspects done well, but from those I've actually used none has impressed me more than the two mentioned above. Bookman has the simplicity down, but doesn't have quite the import/export and features of the other two.