As a recent purchaser...
I decided that Sapphire and Graphite (both 1 year colors I believe) were my two favorite colors, and I wanted stripes.
I also decided that I wanted to track the car occasionally and went for the ACR since it had the extras, and there wasn't that much of a premium over a GTS
I decided I wanted ABS since I was going to drive it on the street more than the track, however many people here say ABS is only useful in the rain which my car won't be experiencing.
I decided a cream puff (post 1999) was acceptable since I wasn't likely to modify the car to the extent that forged internals were required. If I did, even a nice Roe setup doesn't require forged, however I think I'd like to stay NA, as my Mustang is already blown.
Personally i viewed the 2000 as the least desireable year for me, as it gave up the forged internals, and also doesn't have ABS, even though there were some good colors that year.
Interestingly I've found that an ACR with stripes isn't that much more expensive than a GTS without stripes if you look around. That's a $13,000 difference in the original price of the car.
I also looked for 2 years religiously on ebay, cars.com, autotrader, and the VCA classifieds to watch pricing and research what I wanted. Ultimately I decided on a 10K mile 2001 Sapphire ACR with Stripes that I picked up for $54K, a very highly regarded combination that seems to be very popular color around here. I should also mention that while I looked all over the country and was willing to buy from 2000 miles away for the right car, the one I ultimately found was only 35 miles from where I live. Not bad for a car that is 1 of 49 copies.
Hope that helps