If you followed my instructions for setting up MRTG on a Windows platform, you are probably logging every MRTG cron job to %SYSTEMROOT%\system32\mrtg.log. And that log, by now, is probably in the several hundred megabytes range.
I deleted a 700MB log file from an MRTG system that monitors about 30 systems yesterday.
To disable logging entirely, which I recommend once you get things working smoothly, simply remove the “--logging=mrtg.log” bit from each of the cron jobs in c:\mrtg\cron\crontab and copy that to %SYSTEMROOT%\system32\crontab (you will need to halt the cron service before you copy the file over, then restart it again afterwards). You will also want to take it out of your newcfg.bat file, if you use one, so it doesn't get put back in for newly-added config files.
I will update my MRTG Installation article to reflect these recommendations.