What are the best ebook-reading programs/apps?

I have a computer (Windows) and an iPad, but don’t really have any great programs for not just reading ebooks, but organizing them, taking notes, etc. Preferably, it’d be a program that didn’t make me sort by file type – I often can’t remember if I have a book in pdf or epub (or other!) form, so I hate having to search that. And, it’d be great if I could sync my notes from my computer to my iPad and vice versa, but that’s not the top priority. Mostly, I’m looking for a good and easy to use user interface.

Suggestions?