FFMpeg supports FLV 1.1
I still need to confirm this out myself if its true, but looking at the updates in the source it seems as if FFMpeg is now injecting FLV metadata in the latest svn sources.. This means we don't have to use a tool like FLVTool2 anymore after transcoding videos.
Also, they decided a while ago to switch from CVS to subversion. Which is nice, because I use SubVersion for all my projects and now I can use ffmpeg as an external definiation.
The best news is yet to come, FFMpeg has 5 projects in Google's Summer of Code. In this program google funds people who are willing to do open source programming for a project of choice. Among those projects is a VC-1 decoder, which allows transcoding WMV3/WMV9, an AAC decoder (AAC is heavily used in MOV/MP4 videos) and an AMR encoder/decoder (AMR is used in 3GP, 3G2).
Good stuff, I've been following the project for a while now and I'm happy to see its still this active.