I'm not all that fond of the majority of free encoders. I would say HCEnc is maybe better than others in the same price range ($0), but that's about it. Even
TMPGEnc for $37 can be better, although slower. A lot of those free MPEG encoders are designed for speed, not quality.
TMPGEnc was designed for quality, not speed. High end pro software like
MainConcept and Procoder were designed with both quality and speed in mind, with quality being the more important of the two. That's one reason you pay so much for it.
A lot of free encoders are just programmers reverse engineering commercial coding, and then stealing code from each other, to make the next "best" free encoder. I often think there's not a lot of talent -- it's a shallow pool. The real talent is being paid by the software companies. (I would note that some of them did start out making freeware, such as the creator of DVD Shrink, who moved on to Ahead/
Nero software, and then no idea where he went from there.)
Indeed, most of the freeware encoders are very raw, requiring other interfaces to actually use them. Unfortunately, some of those GUIs and front-ends are not made all that well, either, picking poor settings or not fully understanding the encoders. Again, that's the difference between
MainConcept, which comes with a full GUI of all available options, and something like x264, which is either command-line or relies on a GUI/front-end programmer knowing what he's doing.
More often than not, the encoders work okay (not the best quality, but not awful), and it's the interfaces made by others that are buggy. The same is true of many audio encoders, such as Lame, which relies on something like Besweet or what-have-you to actually interface with it. Unless you want to go back to DOS-style computing, that is!