There are tons of options out there. It partially depends on how much you want to budget for the cart.
osCommerce, Open Source Online Shop E-Commerce Solutions - Free, but lacks some quality IMO - I have a site running on it right now and there are some weird quirks and workarounds for things that should be basic.
Zen Cart Support, :: Supporting the Art of E-commerce - Heard alot of good things about this from friends, but no first hand experience
Shopping Cart Software & Ecommerce Solutions: X-Cart. Free shopping cart trial available. - Used this for a site last year - for some reason the templating system really pissed me off...just didn't seem logical, but otherwise it was pretty cool.
Shopping Cart Software by MonsterCommerce - Ecommerce Solutions - Used it in the past and they were great, but it can get a little pricey compared to other options.
The big thing you want to look at is which features you want:
Do you need to ship internationally and how do you want shipping to be calculated?
Are you going to use coupon codes?
Do you want the cart to have clean URLs for SEO (without session ids especially)?
Do you have a merchant account (authorize.net, paypal, etc.) or do you expect the cart provider to give you a merchant account (this limits the options alot)?
Will the products you are selling have multiple attributes (for example: color and size choices)?
If I think of anymore major questions to ask yourself, I'll post them...my brain is fried right now
