I use e-junkie, and I like it alot, if your interested in buliding your own and really cusomizing it I would recommend turnkeywebtools dot com, I have used there script for a dozen clients, works perfect everytime and the features are AMAZING!!
I use GoDaddy Quick Carts. Artidle on this with more info: http://movingaheadcommunications.com/articles/shoppingcarts.html ...they are cheap, have great-looking professional templates and their support / tech team handles everything 24/7 while you sleep. That rocks, no learning curve
Whenever you got stuck, just follow how big guys do... They spend tons of money to set up their stores in the best way to get more sales.. For instance..check out amazon.com Thanks
I like e-junkie but he entry level account only allows you to list 10 products and no download feature. After that the other accounts get pretty expensive