In the case of PDF to Mobi, the Kindle doesn't support reflowable PDF, which means that if you want to "enlarge" the text size and make it easier to read, you basically have to zoom in, and perhaps scroll horizontally to read the entire line if it's a large-sized "page" with a small font. So a Mobi conversion, at least, will let you read the text more comfortably, even if it loses out on pictures and tables and such.
Also, there are plenty of legacy formats from older and now more-or-less defunct models of reader which nevertheless some places like to support because people are still using their old devices.
As for which format is best, well, basically discussions on this boil down to:
