That list could be very long...here are a few that I can remember over the years.
Must slide on a "close" play
No stealing (FP and SP)
No dropped third Strike (FP)
No Infield fly (FP)
Bat the entire lineup
Add an EP (FP)
Players may not slide if they are not wearing a protective slider or pants (same league with the "must slide" rule)
May continue to play shorthanded after ejection
Pitcher's box (SP)
Safety (allow a runner on third to start off the base near the coaches box)
SP Mat
Double plate (similar to Senior SP ) in Co-Ed SP
Time limits (FP and SP)
Run ahead rules