I'd definitely go with 2-pass CBR or 2-pass VBR. It will take longer to encode but will definitely make a difference in quality. Also, you might try adjusting the keyframe frequency. It won't make a huge difference, but depending on the specifics of the video (backgrounds, scene changes, etc) it can affect the quality somewhat. And if you can afford the bandwidth, you may find that upping bitrate to about 500-550 will make a noticeable difference.

We use Windows Media 9, but we're considering changing to Flash because the newest Flash encoders seem to have an amazing ratio of quality to file size, and it is viewable by practically anyone with a computer; WM often has problems on the Apple platform and isn't an option on Linux. Real is a great cross-platform option, but my impression is that it's fading in popularity.