If you have already got a lot of PDFs then you probably have a personal approach to managing all of the content. For example, I keep everything sorted by topic in a directory structure. Here are two ways that seem to provide a better approach (both are interesting): Papers and Digital Editions.
(via Pascal)
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If you use BibTeX, jabref can help index the PDFs. Or you can save them in Zotero.
While I have no experience with Papers or Digital Editions, I find Zotero to be an excellent Personal Digital Library.
I supports items being in multiple locations in a topical hierarchy of folders for those tricky papers. e.g. Does web programming with continuations go under web programming, or language features?
It also has full-text indexing, tags and can import and export(for backup or transfer) data from/to a variety of sources.
PS Zotero is a firefox plugin, so it gets the metadata when you download the pdf, rather than you having to type it in.
Thanks Stephen and anon.