Bukkit

Many ideas for flags:
PreventHunger, Stops player taking hunger/saturation
PreventGrassSpread, Stops grass spreading to blocks in protection
PreventDragonEggTp, Stops DragonEggs teleporting into a protection or anywhere while in a protection
PreventLeafDecay, Stops leaves decaying
Flight, Allows flight for all players in protection
DenyEntry, Denies entry to anyone without access permission
DenyExit, Denies exit to anyone without access permission
PreventLightning, Stops all lightning strikes in the area
PreventHealing, Prevents players healing in area
PreventDeath, Prevents players from dieing in area
PreventPortals, Prevents nether portal and end portal use in area
PreventItemDrop, Prevents items being dropped
PreventItemPickup, Prevents items being picked up

Thanks for the ideas! Out of the ones you've suggested I'm going to be adding:

Quote from CodeNil:

PreventGrassSpread, Stops grass spreading to blocks in protection
PreventLeafDecay, Stops leaves decaying
PreventPortals, Prevents nether portal and end portal use in area

Feel free to make a plugin that adds the rest if you would like.