How to organize my 1000s of PDF?

One possibility is Calibre.

It is an ebook management program which permits conversion to various ebook formats but is cross-platform and can manage databases of pdf files (and not only).

If you decide to install I suggest you do so manually as the version in the repos is not very up to date. Follow the instructions on the site.

A screenshot:

Another possibility is Zotero

It is is bibliography manager but permits adding book details directly through a browser Amazon.com and other sites, pdf attachments and more.

To import the pdf's into Zotero you can see this page.

I use Docear. Mind-mapping is the mode which I prefer to explore tagged (hierarchical) notes and references. The way they implement hierarchical node trees, it is effectively tagging.

The UI for building out mind maps is fast. Though there is some learning curve to overcome at the beginning, it pays off in spades when you actually index your material in a way which primes your recollection later on. It is the closest thing to augmented memory that I have found besides the Google/Wikipedia/[askubuntu]/etc. combos. =)

http://en.wikipedia.org/wiki/Docear