I’ve grown increasingly frustrated with EndNote, its awkward interface and buggy Word integration. I’ve looked at a few alternate solutions: Mendeley, Papers, CiteULike. I ended up settling for Zotero, which I now love.
I don’t think it makes any sense for a citation management software to use ask you to use its own internal search engine. There’s already a ton of excellent search resources: Google Scholar, PubMed, Scopus. The right time, in my opinion, to enter a citation into a database is right after you’ve read the abstract and decided it was relevant. That way your citation database can also act as a reading stack. Since you browse for papers in a web browser, it only makes sense that citation software should be tightly integrated with a web browser.
Zotero is a well integrated Firefox plugin that allows you to add references as you are browsing the internet. It works on Windows, Mac and Linux (Ubuntu is shown above). It works on multiple sites: Google Scholar, Wikipedia, PubMed, Nature, Neuron, J Neurosci/phys, Amazon, etc. When you see a referenced article that you like, you click on a button in the address bar and it adds it to your list of references (quite similar to how one manages bookmarks). It parses the information available on the site and formats it appropriately (it reads authorship information, title, journal, abstract if available, etc.). You can add notes to a reference, attach a pdf (or have it do it for you automagically), link articles together, put stuff in folders, add tags, etc.
Perhaps its most useful feature is automatic synchronization between computers. I often think about research ideas on my way home and do a quick search for interesting references on Google Scholar before going to bed. The next day, I can access all the references I found from work and print them up. I encourage you to take two minutes and watch the introductory video on the homepage, it’s very convincing.