The dam programmers become a necessary evil. Why? well, because the tunes can always be changed as you mod the car, they work well as a code reader, they are a must for a gear swap (why waste money on another calibration device when you can just apply the $100 towards one of these), and are a must if you have an automatic.
I have run the mill with my car. I have had a diablo chip (crap, could never get the tune right); a superchips tuner (the car pinged like an SOB cuz of my mods and it could not accept a custom tune), SCT Extreme Flasher (worked great cuz you can store three custom tunes and have tunes emailed to you), and a 4 Position SCT Switch (this is what I use now. Great device if adding nitrous).
Check out this thread that I wrote at another site. This might help you understand these tuners:
http://www.mustangtuningforums.com/showthread.php?t=19
I say anytime is a good time to get one because you will probably end up doing int eventually anyway.
As far as good "bang for your buck mods", I say X-Pipe, UDP's, K&N, gears, and of course nitrous. If you can get good deals on stuff used, I think the plenum/TB swap is a great mod too, just not worth $400. But at $200 used, that's another story.
Harold and I will split on the muffler vs catback discussion. Why? A nice catback will run you $350. Two good mufflers will cost $120 plus some labor to cut-out and install and then the car looks hacked-up. A nice cat-back also gives you larger pipes and will be in stainless. I think it's worth the extra $200 unless you are really on a budget.