Hi Edalgo,
Videora iPod Converter and 3GP Converter are very similar, infact, they actually use the same ffmpeg core to do transcoding. That said, we recommend that you avoid 3GP converter and use the Videora iPod Converter. Now we know this sounds a little biased so here's why:
Short Answer
3GP Converter is currently intended for the PSP while Videora iPod Converter was designed with the iPod in mind.
Long Answer
1. The PSP supports only 2 framerates. 14.985fps and 29.97fps. A lot of video out there is not one of these 2 framerates. This includes movies, tv shows (23.976 fps), overseas video formats (PAL 25fps) etc. When converting videos using PSP-based encoders, these encoders will force the source framerate to one of these two PSP supported framerates. This #1 leading cause of audio sync issues when encoding PSP video currently.
According to the specs at least, the iPod is more graceful in handling different framerates. Videora iPod Converter simply uses the source framerate and does not attempt to change this in the resulting file which means a higher probability of not having audio issues.
2. Same deal for Audio Sampling rate. PSP only supports 24000 kHz for MPEG-4 SP video and 48000 kHz for AVC/H264.
The iPod will likely handle a multitude of audio sampling rates and does not force a rate onto a video.
3. AVC/H264 encoding is broken in 3GP Converter. Try encoding video at the different bitrates. If you check the bitrate of the files you will see they are all encoding to the same bitrate even though you changed it.
AVC/H264 support for multiple bitrates and Qscales has been tried and tested for months in PSP Video 9 and is working fine in Videora iPod Converter.
This isn't it, the reasons go on and on, but we'll save you the reading (and us the writing
and we hope this was enough to convince you.