Lots of us are still using Roe's VEC I, II or III.
It has some draw backs but for a LONG time is was the best, most affordable option out there. The down sides are that you can fry it if you get water in it and its hard wired into the car (I have mine covered). It doesn't recalibrate the pcm. I think it modifies the signals that the pcm reads or sends. The upside with the VEC is that you can data log off it and you can control other devices with it, like water **** injection or nitrous. It is a great option for FI.
I have heard very good things about the SCT. One of the tuners or vendors can give you better info on it than I can, but I think it actually reprograms the pcm. The down side is that it has no capability to control w/m or nitrous and I don't think you can data log with it.
If you are just doing bolt ons and want to re-tune and go, the SCT is probably best. If you are going FI or nitrous you might want to look at other options.