IMO - FLV is the way to go.
There are pleanty of SHAREWARE versions of FLV players that are SWF's that run accross all platforms and all versions that call the FLV - regardless of codec. Here is one:
http://flowplayer.sourceforge.net/
FLASH MEDIA SERVER 2 is now available, and allows you to stream or download videos to end users. There is alot of controle as far as what viewers are able to do as far as copying or saving FLV files. It will also convert to FLV serverside. This is great for VOD.
http://www.adobe.com/products/flashmediaserver/
Also - the player saturation is best with FLV's. Because roughly 96% of all internet connected computers have the SWF player and only about 70% have the WMP player - FLV's have a greater saturation level.
With regard to video quality.. the newer FLV codecs do quite well. You must keep in mind that if you are converitng to FLV's - be sure you are converting NON-LOSSY files, otherwise you will end up with a compressed-compressed file and that is crappy viewing.
Here is some reading:
http://www.adobe.com/products/flashmediaserver/