We have been working real hard to transfer our old HTML/PHP website to Drupal (about 1,000 pages.) Now it is fully working and it of course uses Ubercart for its shopping cart. It works greatly! We already have several customers using this module and Drupal with success and are more than happy to start using it ourself.
Also, we offer a PayJunction module if you have a merchant account with that company (we can also sign you up!), you can process with PayJunction in minutes! (time to enable the module, enter your login & password, you're done!) We have a Test mode that is only accessible to select user roles so you can test your PayJunction system at any one time! The UC Recurring Fee module is fully supported.
Note that our use of Ubertcart is to sell you Drupal modules! That way, you can extend your Drupal sites with the least effort (instead of re-programming everything yourself... if you could!?) Our hottest module is MO Auto add terms which is the only module I know of that works correctly and will actually add terms to your nodes without you having to do anything (real cool! you should try! I have it on a very large site, over 100,000 nodes and I could not imagine fixing the terms of that many nodes without that module!!!)
Want to know more? Just ask below and I will come back to answer your questions! You can also drop by our website and have a look. Drupal stuff are under "Professional Products" -> "Drupal".
You think our site has problems? I also welcome criticism. Post a comment below and we'll chat!