Free stuff I cannot do without: Skim

All I want to do is to be able to highlight my PDFs so that I don't have to print it and underline it manually.

Skim does this, and more. Not only does it let you highlight text, it also lists all your highlights in a column on the right. (See screenshot above.) It lets you insert notes, both sticky-style and inline.

The inbuilt search engine is sweet too. You can search the text of the PDF (search bar on the top of the left panel), or you can search through just your highlights and notes (search bar on the top of right panel).

Combined with Yep, an iTunes-like application that tags and organises your PDFs, you are good to go. Yep costs US$34. I may buy it if I get a scanner.

Skim and Yep are Mac-only apps.