I personally use fastAmazon, and it's the best. I have some stores setup if you want to see them. The script is super basic, but it works great and is really easy to modify. here's one of my stores: http://notaindustries.com/amazon/skateboarding/
I'd say that associate-o-matic is the best. I've fully integrated associate-o-matic with wordpress and it works wonders.
My vote is for Fresh Store Builder. It has a one time fee, so all the profits are yours, no subscriptions. Also it is very actively supported and being enhanced. Well worth it!
I wrote up a comparison of Amazon store scripts. Based upon comparing and using them, my vote goes toward the following: Amazon Niche Script - very unique features and well designed. Fresh Store Builder - Very well supported and uses modern script, Ajax, for functionality and design. Easy to set up and use. Amazon Products Feed - It's free. But that's about it.
Hey my quick input on amazon affiliate program and amazon store scripts. I been using amazon for over 5 years now and tried a lot of different scripts. Some of the more known ones are amazon o matic and reviewazon witch is for wordpress stores. At first I made very good money using amazon o matic script. I had a lot of sites up and daily sales but after a while my rankings all dropped since amazon o matic really doesn't give you any freedom to work on your stores. You can't edit product pages you cant add uniqe content to your site.. Few months ago I found the best amazon script and was lucky to get in as a beta testing. Script is called Fresh Store Builder. I have a link in my signature for more information. This script is great just take a look at one site i did www.1shopelectronics.com and I have many more but will share this one store i made quickly. Building stores is very easy and fast using the backend control panel. There is new videos out now that show you how to do certain things with the script. Plus the script has a 30 day money back policy. They also have a private forum and I am on there a lot helping new members get setup. So good luck with witch ever script you pick.