I'll cast my vote as well for LaTeX, perhaps with an extra vote for lyx as well (started with LaTeX, but find lyx speeds things up).
More importantly though, I'm casting a huge vote for BibTeX. Get a frontend to take care of the syntax for you. Once you do that, it's a lifesaver. Pick a reference style once and all you need do is drop a quick ref command with the bibliography entry's name and it build the reference for you, adds the entry into the bibliography (properly formatted and placed), and generally takes care of everything. References are often a chore that distracts from including the content you want; BibTeX makes it simple.