https://wahmcart.com/ - Very solid company and may be perfect to fit your needs.
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I am not very clear on what do you mean by merchant checkout program. If you mean merchant account there are quite few options depending on what you sell and where you sell. If you sell physical products and primary customers are within US you can use thirparty providers like paypal, 2checkout or google checkout. If you do more than $1000 a month in business you might want to checkout merchant accounts. start with your bank , usually they resell for some major companies. Major gateways are authorize.net , bluepay etc.. I wrote down pros and cons of few merchant accounts at http://www.iscripts.com/blog/2009/08/accept-payments-online/
If you are looking for shopping cart software and very technical checkout shopify, volution and yahoo stores. If you can create your own shopping cart, there are many options to go including a number of free opensource solution and very cost effective solutions.
http://www.hotscripts.com/category/php/scripts-programs/e-commerce/shopping-carts/ has bunch of applications you can use.