Compare Directory Tree
Solution 1:
Meld is a very good graphical diff tool (and more):
meld dir1 dir2 &
Solution 2:
diff can compare directory trees, too.
diff <dir1> <dir2>
Or if you don't want to see the files content differences:
diff -q <dir1> <dir2>
Some graphical tools available in Ubuntu repos: dirdiff, fldiff, kdiff3, meld, mgdiff.