Got me stumped on this one lol, to get them off the map itself you can just hit clear map, but i don't have a clue on how to actually remove them from the list. Maybe theres something you can do on the computer then just sync up?

man lol, no one can figure this one out. Maybe try removing and reinstalling google maps? idk if you can though because i'm pretty sure it comes on the phone and you can't take off other apps that come on the phone

First post here.  Hello!
 
Settings > Applications > Maps > Manage  Applications  > select all > scroll to Maps.

The "Clear Data" button will remove all the applications data:  including files, settings, accounts, databases, etc...   

Next Map launch will be like the first, but at least all those previous location and direction layers will be missing.

~Mike