I think iBooks is a better app than Stanza (notes, bookmarks, PDF capability) and you can get your EPUBs in there via iTunes (even ones bought from other stores such as the one my startup runs, fifobooks.com).
Frankly, all the readers I've used fall short when it comes to library management. I want something like iTunes (only better!) both to manage my library and create and manage reading lists. Right now everything just goes into one big pile that takes _forever_ to scroll through (I've around 800 titles in iBooks and several hundred in Stanza). iBook on iPad actually has crashed (!) a couple of times as I've gone scrolling from the top of the alphabet to the bottom. I'll admit I'm pushing iBooks harder, but that's because I expect so much more from Apple ;)
The best desktop solution I've found for PDFs (and cbr/cbz comic files) is a comic book reading program called Comicbook Lover. I use it for PDF management (okay, I manage my digital comic book collection with it too...) It works very much like itunes. If they would add ePub support to it, and change the name, they could rule the world, at least for a while. Unfortunately their iPad and iPhone/iPod Touch app is woefully lacking in the very features that make it work so well on the desktop.
Edit: And I do a slow burn every time I go to add documents to my iPod Touch or iPad. Syncing through iTunes is just _stupid_. I understand this is a problem with _many_ apps on the iOS platform, and that there are political and commercials issues involved, but I don't care. Apple needs to work this out, post-haste...
Are these mostly for reference, or are they on your to-read list?
Most of the reference titles I have are in PDF format, though. I've been using a couple of different PDF readers on the iPad, none of which do everything that I would like. When the new iBooks comes out for the iPad, I'll give it a go as a PDF reader as well.
The amazing thing is that _all_ the books on the iPad, all 1000+ spread across several programs, take up less than a Gig.
I like the interface and usability of Stanza better. It does have PDF support, annotations and bookmarks. You can load your own ePubs and PDFs into it through iTunes. It has nice dictionary features, brightness controls, themes, support for third-party libraries.
Overall seemed like a much more mature app than iBooks for the short time I spent with iBooks so far.