I've got to put my vote in for RANT.
It has none of the graphical aids of the likes of FS2002 et al but I feel is offering something far more specific and relevant to actual IR flying. The version I used a few years ago leading upto my IR helped a huge amount just in doing the included lessons and getting my head straight with things such as dip, gate positions in the hold, hold entry, procedural approaches etc. Getting these things straight gives you just those few moments extra capacity whilst actually flying, which I know I needed!!!
Gotta say I didn't have FS at the time so don't know how much that would have helped.
As an aside how much do they charge for RANT now? We were given it gratis as part of the course.