"Erase all map data" deletes and replaces the map with a new map, just like creating a 'New Blank Map'.

"Erase tile data + doors + NPC instances" deletes the map layers, wallmap, foemap, zones, doors, doorlinks and NPC instances. It leaves the NPC definitions and General Map Data intact. This is useful for copying just the NPC definitions from a map.

"Erase NPC instances" deletes all NPCs placed on the map, but not any NPC definitions.
Notice that you can delete all copies of a specific NPC by pressing DELETE while in the "Edit NPCs" menu.

Other options are self-explanatory:
"Erase NPC instances + definitions"
"Erase door positions"
"Erase doorlinks"

Of course, none of these options delete Global NPC Definitions.

If this map is the last map, an additional option appears, "Delete map entirely", which reduces the number of maps by one.