Both readers have their strengths and weaknesses, which is why I'm still playing with both. iBooks is certainly the younger of the two and I expect it to pass ahead, especially since the Stanza folks seem to be under the sway of Amazon, which has a vested interest in the fight. PDF capability will certainly be a big plus for iBooks when it comes to the iPad. I'm running the new version on my iPod Touch, but PDFs on such a small screen aren't that useful, at least to me.
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...