Delete waypoints, save & load missions, drag & drop.... it's really getting there!
Feel free to download and try it out. I have not yet tested with the ArduPilot itself so read/write may not work.
Config Tool Download
If your map on the right is blank or you see a series of odd buttons where the map should be, you'll need to look into issues with your Internet Explorer and Google Maps. See here for instructions: Google Maps Troubleshooting
Please also check out this blog post GPS Emulator
for info on how to use the GPS Emulator that is now included with the ConfigTool.zip