Any
 Video Converter is a really easy to use free video converter - just 
choose your source file and output format and go. If you need them, 
there are lots of advanced options too like batch conversion, file 
merging, and frame cropping.
Input Formats: 3G2, 3GP, 
3GP2, 3GPP, AMV, ASF, AVI, AVS, DAT, DIVX, DVR-MS, F4V, FLV, M1V, M2P, 
M2TS, M2V, M4V, MKV, MOD, MOV, MP4, MPE, MPEG, MPEG1, MPEG2, MPEG4, MPG,
 MPV, MS-DVR, MTS, NSV, OGG, OGM, OGV, QT, RM, RMVB, RV, TOD, TP, TRP, 
TS, VOB, VRO, and WMV
Output Formats: AVI, FLV, MKV, MP4, MPG, SWF, and WMV
The
 only thing I didn't like about Any Video Converter was the window that 
appeared after each video conversion suggesting that you upgrade to the 
"pro" version to enable more output formats.

© DVDVideoSoft Limited 
Free Studio Manager is a collection of integrated video converter programs. Just click 
DVD and Video from the main screen and then choose what video converting activity you'd like to complete.
Free Studio Manager is light on options but is super easy to use.
Input Formats: 3G2, 3GP, 3GP2, 3GPP, AMV, ASF, AVI, DVR-MS, FLV, M4V, MOV, MP4, MPEG, MPE, MPG, QT, and WMV
Output Formats: 3GP, AVI, FLV, MP4, SWF, and VOB (DVD)
During setup, Free Studio Manager asks if you'd like to install the DVDVideoSoft toolbar but it's easy to skip.
 
 

© HandBrake Project 
HandBrake
 is an incredibly easy to use free video converter that's most useful 
for converting pretty much any video file you might have into one 
that'll work with your mobile device.
Input Formats: AVI, FLV, OGM, MP4, MOV, MPG, SWF, WMV, VOB (DVD), WMV, and XVID (HandBrake's website says 
"Most any multimedia file" - let me know if you can confirm any more)
Output Formats: MP4 and MKV
 
 

© YouConvertIt 
YouConvertIt
 is an online video converter service that will convert many popular 
video formats. You just upload the video file and wait for an email link
 to the converted file.
Input Formats: 3GP, ASF, AVI, FLV, MOV, MP4, MPEG, MPG, RM, SWF, and WMV
Output Formats: 3GP, ASF, AVI, FLV, MOV, MP4, MPEG, MPG, RM, SWF, and WMV
The
 biggest disadvantage with YouConvertIt is the wait time to upload the 
video and receive your email. Their 300MB file size limit is certainly 
disappointing as well considering the fact that many video files can 
exceed this size.
 
 

© Zamzar 
Zamzar is another online video converter service that supports most common video formats.
Input Formats: 3G2, 3GP, AVI, FLV, GVI, M4V, MOV, MP4, MPG, RM, RMVB, VOB, and WMV
Output Formats: 3G2, 3GP, AVI, FLV, MP4, MOV, MP4, MPG, and WMV
The
 worst thing about Zamzar is their 100MB limit for source files which is
 a significant drawback considering the large size of most video files. I
 also found Zamzar's conversion time a bit slow, even for an online 
video converter service.
Zamzar Review and Link