In my experience, I've found these differences:
- Kindlegen does not produce an in-line TOC. Calibre does. However, it is placed at the end of the document, which displeases some book designers.
- Kindlegen includes the "source document" (e.g. the starting epub) in the mobi, thus doubling its size. There are scripts available on this site to strip the source from the mobi.
- Calibre used to have a "bug" whereby Amazon's DRM could not be applied to the mobi. I think this has been fixed for some time now, though.
- Under certain circumstances, a kindlegen epub -> mobi converted mobi will have two instances of the cover. One as the cover itself, and one as the first page of the document. I think Calibre avoids this.
Actually, for my own use I like the Calibre conversion somewhat better. But for commercial applications (Kindle store) I pretty much have to go with kindlegen starting with a "specially crafted" epub to get the results I want. Which is why I'm a little hazy on the details of Calibre conversions.