Friends of mine just completed the Great Loop (Lake Michigan to Mobile, Gulf ICW, East Coast ICW, Hudson River, Erie Canal, etc back to Lake Michigan) and anchored about 1/3 of the time. They felt they could have anchored much more often. I have done the East Coast ICW a couple of times. Sometimes anchoring and sometimes going through the night without stopping. Anchoring opportunities vary with where you are. I think you have to stop when in the canals, but there are often places to tie up at the locks or at town docks without paying marina fees.
Check out http://www.greatloop.com/
and other sites for great reference information.