It depends on what you are trying to convert as well as the quality you want from the final encode. Most people around here tend to take a few extra steps to ensure quality and reliability. There are simple utilities out there that will do all of the transcoding steps automatically, but honestly I prefer not to use them and I do not know of any good recommendations.This is how I do it:
1a. For lossy sources (generally mkv, mp4, mpg, often avi), use avisynth
to make a script which reads the source.
1b. For DVD or Blu-ray, it takes a lot more in-depth information than I am willing to type right now. Feel free to ask and we can help you out though if this is the case.
2. Open the script with Virtualdub
and then render it as a lossless avi. You can use uncompressed avi or a variety of lossless codecs, but I recommend Lagarith
(for UTVideo, click on the link near the top that says 'x86').
3. At this point, you can encode to the final format of your choice. For online distribution, Zarx264gui
is easy and will make a nice mp4, or even mkv now I think. For a specialized device, like a PSP or iPhone, I use Handbrake
Let me know if you need me to elaborate on any step. I realize that this seems complicated, but it will result in very good quality. Perhaps someone else has another method?