Sure ..
At command line
Code:
for /r %1 in (*.mobi) do "c:\Program Files (x86)\Calibre2\ebook-convert.exe" "%~dpn1.mobi" "%~dpn1.epub"
In a batch file
Code:
for /r %%1 in (*.mobi) do "c:\Program Files (x86)\Calibre2\ebook-convert.exe" "%%~dpn1.mobi" "%%~dpn1.epub"
In either case it will go through all directories starting at the current directory and convert mobi files to epubs.
The difference in the two command lines is due to the interpretation of the % symbol at the command line, and in a batch (or cmd) file.
The weird stuff
%~dpn1 is just extracting the drive, path and file name from the whole file name; ie dropping the extension.