I use ecart with GoDaddy and have been for a few years.
Whatever you do....DON'T USE COLDFUSION.
GoDaddy has a lot of problems with it.
I am switching all of my sites to PHP and don't yet have any experience with GoDaddy and PHP/Mysql. But they definately support it.
Good Luck and stick with it! Between the great WA support and GoDaddy support you'll be up and running in no time!