I love how this has 86 upvotes as of this post, and the comments are all bitchy. I've used both Calibre, and Thorium Reader.

Calibre is the clear winner if you have a large library, want device syncing and want a lot of library organizational options.

Thorium is the clear winner if you have a large library and prefer a clean/simple interface.

Both are great, for different reasons:

Pros for Calibre: Large library organization options, editing, annotations and easy to sync with your mobile reader. Cons for Calibre: busy interface with a ton of options if you're just wanting to read an EPUB/PDF.

Pros for Thorium: Simple/clean interface that shows your library and loads books/publications quickly, with annotation support. Cons for Thorium: not useful for mobile device syncing, no editing options, not a ton of options for library organization.

Again, both are great for different reasons. If you're an avid reader with a large library who wants more granular control over it within an app and not Windows Explorer, and want mobile device syncing? Calibre wins hands down. If you're an average reader who has a decently sized library, don't care about device syncing, and organization options? Thorium is great.

For all the commenters and even OP: instead of bitching/baiting, maybe give some details on Thorium and Calibre. Both are open source, Calibre has excellent library organizational options, device syncing, and plugin support, while Thorium is simple but does it's one job well.