Squeeze is the best tool for doing this, but it will take a LONG time. Compressing HD to web FLV produces some excellent images, but its not something you start and finish within the same evening. Beyond the normal tips for FLV encoding such as framerate, size, and bitrate, there isn't much to say.
Also, HD is normally in the 709 color space, while Flash and other video expect 601. ProCoder is the best app for handling that conversion. It doesn't have native Flash, but can work with the Macromedia export component.
That said, the color space conversion is only critical when color accuracy is critical.