Assuming you have two programs that process the two files, process_in.exe and process_out.exe:
for %%f in (*.in) do (
echo %%~nf
process_in "%%~nf.in"
process_out "%%~nf.out"
)
%%~nf is a substitution modifier, that expands %f to a file name only.
See other modifiers in https://technet.microsoft.com/en-us/library/bb490909.aspx (midway down the page) or just in the next answer.