If you mean directly and automatically on your iPhone, there's been some talk of companies working on real-time transcoders for FLV (Flash Video) to Quicktime, which streams natively on the iPhone, but I don't think we've seen a working/public version of this yet.
If you mean can you take a Flash video you've saved on your hard drive and convert it, and sync it to your iPhone/iPod, absolutely. Many transcoders, local or web based, can handle the basic FLV file and spit you out an iTunes compatible version.