If you have a Mac and you ever read large PDFs such as standards documents then you might think about checking out Skim.app. It lets you take notes, has sensible search highlighting, and has this crazy reading bar to help you keep your place when you are looking back and forth between the document and something else.
For some reason Preview.app always has flaky search for me. The cmd-G “repeat search” command only toggles between the first two or so results rather than all of them. Skim.app actually works like I expect and it highlights the results with easy to see red ovals and yellow highlights.
The pdfsync functionality seems like it would be cool but I haven’t gotten it to work correctly yet. It seems to give the wrong file and line numbers for a test PDF that I’ve been playing with. OTOH, I haven’t spent very much time getting it to work.