Running maxfilter manually for all your dozens of files is little joy, especially because you frequently have to re-visit your settings and reapply it. Attempts have been made to automate the process. Please, post your ideas, designs and strategies for this here.
One suggested strategy is to first run the MF on the first 20 second of data just to identify bad channels automatically, and then pass the list onto the proper maxfilter with autobad turned off (as it does not seem to work properly anyway). The obvious disadvantage is that you only rely ona small portion of data for marking your bad channels, whereas they have been known showing up (and disappearing) randomly throughout the recording. If this does not deter you, click here for an example of a Perl script that will do just that. Naturally, it can be adopted for doing almost anything.