When you create scientific reports or you just prepare for exams you usually have to go over a whole bunch of papers,
lecture notes and websites.
old way is to print them out and use some highlighter to mark the most important parts. But often I prefer to just
highlight the pdf files directly on my notebook while reading or flying over them. You also save the environment by not
printing everything which you probably will throw away anyway later on.
On Windows and Linux I used to do it
with the build-in mechanism supported by MS PowerPoint but just for PP slides of course. For the rest I used Jarnal
a cross-platform Java-based app. However Jarnal did never really convince me. It is more suitable for tablets rather
than for normal notebooks. But now I found Skim
Skim is a PDF reader and note-taker for OS X. It is designed to help you read and annotate scientific
papers in PDF, but is also great for viewing any PDF file.
..and it's Open Source wherefore
it's always worth mentioning. A list of features can be found here
Beside an excellent UI experience and the capability of support of interaction with LaTeX, SynTeX etc it is really cool
that you're PDF's itself won't get polluted by your annotations. This means you just open your pdf file with Skim, put
your annotations and highlightings and save it as usual. If you then open the pdf just normally with Previewer you
won't see anything of your previous edits. Of course there is also the option of exporting your edits.
Btw, for direct highlighting of
webpages you might consider Scrapbook
which is a nice
add-on for Firefox.