In Calibre You can select several books at once, and hit convert. It is an old feature, described on the official blog:
Bulk convert: Calibre allows you to convert books in bulk. You can
select a set of books, all of which may or may not be in the same
format, and convert them all in bulk to a different format. So say you
have a kindle and you have a number of books in EPUB, RTF and PDF
formats. You can select them all. Then click the "Convert books" icon
or click the little arrow next to the "Convert books" icon and choose
the option "Bulk convert". A new window opens. At the top right
corner of the window you can set the output format, which in this case
would be MOBI.
If You are on Linux, You can also write a script to utilize Calibre's command line capabilities.