Another of my favorite tools for this stuff is Stray Lines. Often when a face does not close it is because the lines don't actually meet up correctly. So label stray lines goes through and puts a little text tag at each line end that does not meet another end. So you can see VERY easily all lines that don't actually touch. Sometimes theya re obvious, but often they are virtually impossible to find w/o this tool.
Chris
EDIT: To make it more clear, once the lines are labeled, it then makes it clear where to go to start filling in the missing segments, deleteing, extending lines, etc.