WooCommerce is a direct knock of of JigoShop, although Jigoshop has a much nicer look and feel, why the woocommerce hackers changed that I have no idea.
Ive tried WP e-Commerce VS WooCommerce. and I like WP eCommerce becuase it doesnt have the problems WooCommerce has, However WooCommerce has a few nice features, and I dont mean the stupid Bells & whistles they add rather than resolving the important issues.
The main problem is WooCommerce doesnt work with many themes, so your nearly forced to pay alot and become a member of their site to access the themes. Personally, I see many flaws in woocommerce, most are tiny, but even more reason they should be corrected. I also see lots of features on woocommerce that really dont work the way I would expect them to. Like the shipping options, WP eCommerce allows real use of services like USPS, and UPS, whereas WooCommerce does not. In Fact, a friend purchased a shipping add on from woocommerce, and it didnt work, I wrote to them, and still to this day Never heard back from them.
Also, unless your site is very bland, and doesnt use a lot of CSS, they woocommerce would be ok. Otherwise youll spend days revising their CSS file to suit your needs and to remove all the crappy box shadows and junk.
I Highly recommend trying each programs attribute features, this should make your decision on which one works for you.
In the end the best thing to do is take the time and try them both. WP eCommerce is much easier to use.
My advice is if you wont want to get frustrated because it doesn't work the want you want, or just dont have time to mess with it, I would recommend wp eCommerce instead.
Both are free (if you can get woocommerce to work with your theme) so really we cant complain, right. Then again, who wants to spend hours configuring, and adding product just to find out the plugin isnt the best choice.