It depends on how handy you are. I have used the ~$250 ones from Speedway and the ~$50 ones from Amazon. I have also bought rolls of wire from Waytek and done it completely from scratch.
The speedway ones are nicer because every wire is individually labelled every foot on the insulation. You do have to cut to length, put on the connectors, and figure out your own routing. I personally find that pretty straightforward, but I am an engineer by trade so your mileage may vary.
I do remember being pretty intimidated the first time I needed to completely rewire a vehicle. I pulled a painless harness out of the box and stared at the pile of wire for a while. Once I got down to it and started laying things out, it really wasn't that bad.
The other thing to take into consideration is if you are going to be adding any new features (power locks, new radio, turn signals, etc). The stock replacement harnesses I have seen do not have provisions for those, so you would have to figure out how to wire them in yourself. The universal harnesses will have turn signal wiring and extra circuits for whatever else you want to add.
