Are you using a dos command-line based application?
if you, look at the FOR command that DOS/Windows has.
For example:
C:\ROMS\>for %i in (*.bin) do echo %i
will echo each .BIN file independantly for you.
so...
C:\ROMS\>for %i in (*.smd) do smd2bin %i
should run the smd2bin exe for each...