There's several pieces of software that can help you handle this task. I use BibTeX and some related tools myself; another popular software is EndNote. It'll help you keep a database of references with links to the actual paper, your notes and so on, and can let you share your reference lists with others. Like BibTeX, EndNote also has a large collection of style files for various journals and conferences that will format your reference list in the appropriate way. It's worth noting that both reference lists and style files are generally created by the users - us - not by the software developers.
Enter Zotero. It's a paper and citation organization tool, as a Firefox plugin. It's completely free and open-source, and is more at home on the web than any of the earlier tools. I've tried it previously and while it hasn't displaced my current tools yet (old habits are hard to break) it does look very, very promising, and it's steadily becoming more and more popular among academics.
So promising, in fact, that Thomson Reuters (owners of EndNote and a lot of other academic-related property) is suing the makers of Zotero for allowing its users to convert EndNote style files and citation files into Zotero format. Files, worth noting, that were contributed by their users in the first place. More from Crooked Timber
This is exceedingly stupid. Or desperate - EndNote may be losing market share to open tools much faster than people realize. The stupid part is, they are antagonizing their own customer base - they're suing part of it. People whose livelihood depends in part on their citation databases are naturally a little wary about keeping them in a closed format like EndNote's, and now Thomson have given them ample reason to be anxious. They are stating, in effect, that they will do anything they can to prevent people from moving their own data away from the EndNote system. EndNote is an intellectual roach motel - your data enters but it can't leave.
The legal case itself seems to be on very shaky ground even in the US and it certainly has no merit at all in much of Europe (where reverse-engineering for interoperability is expressly legal). But that is beside the point. There is possibly not one single thing they could have done to damage their own product and promote Zotero further than by suing them in court.
This is the same Thomson Reuters that is one of the giants in scientific publishing that are already seen with some suspicion and hostility by the community itself due to their antagonistic stance on open access. If you ever needed a reason not to consider EndNote for your own work, this is it. And take a good look at Zotero; it may be everything you need and more already.