When examining the advantages and disadvantages of a T-tail configuration versus a conventional one, there are really two distinct categories within the comparison. There are the pros and cons associated with the placement of the tail, and there are the pros and cons of the location of engines - two seperate issues (the C-17 is a perfect example). Thus, to summarize:
Tail location pros and cons.
--Stall problems? No.
--General aerodynamics? Average.
--Prone to foreign object damage? Yes (i.e. more so than T-tails).
--Stall problems? Yes. At high AoAs and more importantly when stalled, T-tails are placed right in the path of the wings' wakes, causing the aforementioned condition of "deep stall."
--General aerodynamics? Good. T-tails produce less drag and are generally efficient aerodynamically because they're away from all sorts of fuselage flows and eddies, and the interference drag characteristics are changed.
--Weight? Sometimes greater than normal due to the need for increased structure around the vertical stabilizer area.
--Prone to foreign object damage? Not as much as conventional tails. That's why the C-17 and C-141 have T-tails, I believe.
Engine location pros and cons.
--Ground clearance issues? In some cases yes (particularly with smaller aircraft).
--Internal noise? O.K.
--Acoustic fatigue? Possible flap and wing fatigue.
--Crash safety? Good.
--Propulsive efficiency? Good.
--Longitudinal stability? Good (also delays tip stalls).
--Asymmetric thrust characteristics? Relatively poor.
--Weight? Good (wing bending and torsion relief).
--Wing aerodynamical characteristics? O.K., possible flap/leading edge 'cutouts'.
--Ground clearance issues? No.
--Internal noise? Good.
--Acoustic fatigue? Proable fuselage fatigue.
--Crash safety? Possible problems.
--Propulsive efficiency? O.K. (if positioned well).
--Longitudinal stability? O.K. (not as good in terms of tip stalls).
--Asymmetric thrust characteristics? Good.
--Weight? O.K.; heavy tail, heavy fuselage frames, 2-4% heavier empty.
--Maintenance? O.K. (high off ground).
--Wing aerodynamical characteristics? Very good.
There you have it, tail design in a nutshell!