Here are the ones that are on the top of my head, if I forgot any let me know. Note I didn't list 9/11, don't think it was a false flag operation but I do think it was exploited in the aftermath as if it were one.
False Flags:
Boston Marathon Bombings
Sandy Hook
Jared Loughner/Gabby Giffords
BP Oil Spill
JFK Assassination
Cover Ups:
Federal Reserve
Benghazi
2008 Wall Street Collapse and Bailouts
Osama Bin Laden Assassination