A bit late on this: I wrote a good long while ago about Zotero, an open source reference management tool, and how Thomson Reuters, makers of EndNote, the most widely used (or at least most heavily advertised) such tool was suing GMU, where Zotero is developed, in court. Their grievance was that Zotero included a filter to convert citation format definitions from the EndNote file format and they claimed this was a copyright violation. This was a preposterous lawsuit, made even more so as these format definition files weren't even created by Thomson Reuters at all but by their users.
This lawsuit finally reached the court a couple of weeks ago, and the court promptly threw the whole thing out.
I use Zotero myself nowadays, and while it's far from perfect (the user interface is rather frustrating on a small screen), it is certainly good enough for real-world use. If you need a citation manager I advice you to take a good look at Zotero or other alternatives before locking your own citation and bibliography data up in EndNote. Thomson Reuters have after all shown that they're willing to go to court to prevent you from leaving them once they got you.