One of the most common problems I see at customers is that the IIS logs on the SCCM servers are filling up the system drive.
The log files can easily become around up to 2GB per day on a site server with the MP and DP roles on it, of course depending on many other factors as well, number of computers, polling interval and so on, but still the disks get filled up.
There are two ways of solving this:
1.Turn off the logging in IIS (check first with compliance and security regulations which may apply).
2:Use a script that will delete all log files older than for instance 7 days.
There are a lot of VB and powershell scripts out there that will do the job for you, I have used this one http://www.808.dk/?code-iis-log-housekeeping#ManualJustDelete a couple of times and it works great.
Have you checked the size of your IIS log-files on the SCCM Site system servers lately?