Most FLV's are just h264 in the flash video container. Try using flvextract to extract the audio and video streams:
http://www.afterdawn.com/software/au...lv_extract.cfm
Then just remux the streams in the mkv container with mkvmerge (download the latest version at the bottom):
http://www.bunkus.org/videotools/mkvtoolnix/win32/
You could also mux them in the mp4 container with Yamb.
If you want to re-encode them to make them smaller, you might still need to remux the streams and then use the one-click encoder option in MeGUI.