I just came across a new PDF viewer by the name of FlexPaper. It was developed by the Devaldi group out of Auckland. It has a similar set of features to Adobe Reader, and because it's Flash based it can be embedded in another page (Reader has only a full screen mode).
FlexPaper is an open source app, which means you can edit it to suit yourself. It's not closed like Adobe Reader. It's offered in Adobe Flash or Adobe Flex, so you can install it on a web page and the second so you can integrate it into a program. BTW, both Flex and Flash are dependent on proprietary Adobe technology, so basically you're giving up the closed Adobe Reader in favor of the closed Flash player. But then again, I've always found that Adobe Reader to be a resource hog when run in a browser. FlexPaper doesn't appear to be quite so bad.