June, like kelly said, do not worry too much about MacJanitor...all it does is run three unix shell scripts. They are called "daily", "weekly" and "monthly".
The "daily" script is set to run on your machine at 3:15 AM each day. It cleans up scratch and junk files, backs-up netinfo data, rotates log files and checks your subsystem status. It is not crucial to run this each day, you could go for weeks even months and nothing bad would happen. It doesn't repair or fix anything. Just "cleans" up. The NetInfo backup is somewhat important, but not crucial.
The "weekly" script is set to run at 4:30AM each Saturday. This script does similar maintenance as the "daily" script. More log rotation and it updates "whatis" and "locate" databases (this is used when in the terminal, it does not affect the usefulness of your Mac when in the GUI). You'll never need it, it's for those who use the unix part of the Mac OS.
The "monthly" script runs at 5:30 AM on the 1st of each month and just does some "login" accounting and rotates more log files. Again, nothing that would cause harm to your system if it weren't run. It's just that these log files might get a bit large over time and take up a small chunk of your disk space. Log rotation just trashes the oldest logs. These logs contain system messages, error messages and such. There are system logs, mail logs (they do not contain your email), ftp logs (not applicable unless you'rte running a ftp server) same for web logs, unless you turned on personal web sharing these logs are irrelevant.
So, if you look at the times these scripts run, you know why people say to leave the Mac on overnight. Just understand that the Mac has to be "fully" on and not sleeping. Otherwise the scripts wont run.
If you want these scripts to run, leave your Mac on overnight, let's say, each Friday/ Saturday, or if you prefer, try downloading MacJanitor again and run these scripts at your convenience manually.
