H264 requires QT player 7.+ to play. Windows Media Video might require an upgraded player install. Both require the user to download and install something…will your audience do that?
Flash requires the least effort from the audience…worse case is for them to click OK to update the browser plug-in. The quality of all three is quite close…I like Flash.
Creating good quality web video requires either dozens of hours experimenting or read one of dozens of books on the subject or even better option is
Internet Killed the Video Star by Aharon Rabinowitz
A Guide to Creating Video for the Web
Available at the Cow Store. Highly recommend it.