You can do a month-long search on our site matrix.itasoftware.com and put lists of airports (separated by semicolons) in the "From:" and "To:" boxes.

But as YYJGuy said, the broader you make the search, the more likely it is that we will miss a particularly good fare on a complex routing.

We've been doing some work recently on improving the result quality of month-long searches, so hopefully you'll see discrepencies less often in the future.