Ive personally never even heard of Squirrel Cart and Ive built a few ecommerce sites back in the day.
Ive personally used:
MivaCart (thumbs down) (dont remember cost)
AmeriCart (thumbs up) ($249 a year, comes with its own SSL server)
OsCommerce (steep learning curve and requires much tweaking) (free)
ZenCart (not as bad as OsCommerce, same basic functionality) (free)
The price seems reasonable at less than $200.
They have 70ish listed clients, that could be a good thing or bad (small customer base should = great customer service, or the product blows and noone is buying)
I would safely say that 99% of all the PHP cart systems are customizable to whatever extent you need as long as you know PHP. The big difference in the different "package" PHP carts is the amount of customization and "features" already done up for you.
The amount of products and the amount of options for each product that the website is going to carry, and how to get those into the cart system in an efficient manner would be my determing factor.
I have yet to find a cart system that will handle a large # of products with various options without becoming a huge unwieldy mess during the import/upload of the initial item database.