Here's some common ones:
Differences in airspace rules (speeds, equipment, communication).
Holding speeds/altitudes. When should you start slowing to holding speed?
When are you required to report to ATC, what items should be included?
When is an alternate required, what are the requirments for the alternate?
Minimum IFR altitudes (mountainous/nonmountainous) What is considered mountainous terrain? What amount of terrain separation are you given on the intermediate approach segment?
Fuel reserve requirements for IFR, with one or two alternates.
If you have previous 135/121 experience, know the rules for alternates under those regulations.
Hope that helps.