Well the main functions are the bits that I always wanted in the Civ Editor
So it does copy/paste of a selected area, also you can nudge maps along the x/y axis and add empty space to the edge of a map. Note that you basically need to do this stuff on a bare map - no units/cities/and preferably no start points.
For a world map from scratch I don't see much use from these bits, but if you found a map of europe but wanted to add the ME you could use it to add the space to the europe map and then paint in the new terrain (probably in the Civ Editor)... and stuff like that.
It also has an analyzer tool that essentially provides MapStat like statistics but through the map interface. Useful for balancing, espeically as you can select pretty much any combination of tiles in MapTweaker and then run the analyzer on the selection.