I wouldn't say that the best value thing would have to be expensive you would just need to get a bigger bang out of whatever it was. For me some of the best values just happen to be the small thing that end up getting a lot of use.
I would have to go with the harleygoodies ext. They made a world of differance in comfort.
You know, I forgot all about those. I love them too. And the fact that I got them for free really puts them light years ahead in the cost benefit analysis.
Probably the best and first mod you'll want is a good set of slip-ons. Makes the bike sound 'real' and no tuning is needed until you go into intake changes.
My best has to be the Shotgun shock like several others have mentioned. The ride is incredible and the diversity is great. My second would be my Mustang seat with backrest. I can ride all day on that puppy. Feels like a recliner.