For converting my flv or swf files to video format I use Flash to Video Encoder PRO. I have this program long time and it works fine for me and create video files with good quality (as it's possible from compressed flv to video ) I think you can try it too.
You can use this free online converter. http://www.zamzar.com But it can not convert big files and it does not support batch conversion. It can not join files to one file. It can not convert big files.