MPEG-4 is a superior codec to Sorenson 3, which is likely the codec you were using for your QT movies. Additionally, it's cross-platform compatible, meaning QT or WMP or Real will play it. Its implementation in FCP3 is buggy, though. So make an MPEG-4 and a Sorenson 3 version of the same thing, making the encoding parameters as similar as possible, then compare the outcome. Go with MPEG-4 if it's working satisfactorily.
Like Nick said, anybody not able to play QT movies is way behind the curve. Fuck 'em.
The most obvious advantage of QT is its cross-platform compatability (in terms of the Operating System). It's the most robust of the three media programs in many ways, and is the most sensible choice for web encoding. That said, the Window Media Codec has superior visual quality when compared with Sorenson.