Originally Posted by VGeorgie

No converter based on FFmpeg will give you the best quality, as FFmpeg supports only a very old FLV codec. You want VP6, which Flash 8, CS3, and CS4 support out of the box. Otherwise you'll need to get a cheap converter app from On2.

You don't mention what the bitrate is of your WMVs. To get equal quality you'll need to encode at about the same bitrate. If your WMVs have a high bitrate to start with that can be a problem, because FLVs are meant for streaming, and not everyone has 10 mbps connections.

You need to keep trying different settings until you get something that looks good to you. You WILL likely have to compromise some on quality in order to get a filesize and bitrate your users can handle.