You can try these. They have a variety on video input and output file formats including FLV and MP4:
Free Flash Flv Video Converter
It is a powerful tool to convert flv files to other video and audio formats, such as FLV to AVI, FLV to MPEG, FLV to WMV, FLV to MP3, FLV to MP4 and FLV to 3GP. Free Flash Flv Video Converter can convert batches of FLV to most popular video files with just a few clicks. The output video files can be AVI, MPEG (MPEG1 and MPEG2), WMV (WMV7 or WMV8), MP3, MP4 (MPEG4 and H264) and 3GP (3GPP or 3GPP2). With Free Flash Flv Video Converter, you can set the output file's Video bitrate, frame size and audio channels, etc. Free Flash Flv Video Converter has a built-in video splitter. You can extract only a part of source Flv file to the video format you select. With very simple settings, Free Flash Flv Video Converter can convert flv files easily and conveniently!
You can check it out here
http://www.easyfreeware.com/free_flash_flv_video_converter-9885-freeware.html
OR
Koyote Free Video Converter
Koyote Free Video Converter is one of the most complete programs to convert your videos under numerous formats. Simple and easy to use, it allows easily to extract videos from sequences and accomplishes conversion with pre-visualization.
Supports large range of formats like AVI, MP4, iPod, PSP, 3GP (mobile phone format), Zune, iPhone, FLV, MKV, WMV, ASF, MOV, QuickTime, MPEG, RM, VCD, VOB...
You can choose to convert only some parts of your videos. It allows to set the Start Time, end time or duration that you wan to extract.
You can choose to only extract the sound of your video into MP3, WMA, MP2, AAC...
Extremely fast conversion speed.
You can check it out here
http://www.koyotesoft.com/indexEn.html
Download link : http://www.koyotesoft.com/appli/Setup_FreeConverter.exe
OR
SUPER (Simplified Universal Player Encoder & Renderer)
SUPER is an easy-to-use Multimedia Encoder and Player.
It's a simple, yet very efficient tool to convert or play any Multimedia file. It supports any Multimedia file format. SUPER is the fastest and simplest tool to encode full-length movies to any other format without any time or function limitation. It does NOT require any additional external codecs. They're all built in!
It supports the following formats as input source file:
- Input Image Sequence: jpg, pgm, png, ppm (with sequentially numbered-ONLY filenames)
having the same filename numbered-ONLY format. Example: 0001.jpg --up to--> 0999.jpg
note that this format will NOT work name_0001.jpg --up to--> name_0999.jpg (take out name_)
- Input Video format: 3gp, 3g2, amv, asf, avi, dat, dvr-ms, fli, flc, flv, m2ts, mpg, mkv, mov
m4v, mp4, nsv, ogm, qt, rm(vb), str, swf, ts, trp, ty, ty+, tmf, viv, vob, wmv ..
- Input Audio format: aac, ac3, amr, flac, mmf, m4a, mp2, mp3, mpc, ogg, ra, wav, wma ..
- Input AviSynth Script Files: avs. To write a script and specify advanced encoding commands using AviSynth scripts!
You can check it out here
http://www.erightsoft.com/SUPER.html