That's a good question. For me, it depends more on the deal and what I'm getting. I have swapped these motors with "0" miles on them to "just over 100,000", as I was told. These are the greatest motors ever, imo. But like all motors, one with 10000 miles on it that have all been spent at the red line may not run as well as one with 100000 easy miles with services done all the time. Most of the time, you will not know how well the motor has been treated. So it's a bit of a gamble.
So I'm more concerned with the price and the bolt ons that come with it. Sometimes the bolt ons can be overlooked. You can spend as much buying the bolt ons after the fact as you can the used engine by its self. If you know you will be doing custom bolt ons, save money by buying a motor with no bolt ons. If you know you will be making a custom harness, don't pay extra for one that comes with a harness. Likewise, if you want a cheap "thinned" out harness make sure you buy a motor with a harness included. They are HARD to find in good shape afterwards. Also, a motor that has been sitting for a long time will most likely have varnished injectors. If they can't be cleaned you'll be looking at buying a set. That cost could have put you into a better engine to begin with.
The bottom line is that the motor is the cheap part of the swap. We're talking $1-2000 in a swap costing $5-10k. Getting the whole thing wrapped up and finished just to find out the motor is bad stinks, but is not the end of the world. I have cranked a few of these motors over for the first time, having no idea what would happen. They've always run, but I have expected the worst.