I wasn't a big fan of the early releases, but I like the new version of the PDF Browser Plugin for Panther. Now I use this to have a quick look at a paper, then save it (named AuthorYear) into a folder with a Folder Action attached, which automatically opens up DevonThink and stores the paper for reference and searching. To read the paper in full, there's a menu option to open it in Acrobat and add comments and highlighting there.