No problem. There are no third-party modules used at all. I wrote 40+ modules, a few skin controls with about 250 tabs, including the store-front. Some of the modules I wrote were ports from an asp.net application I wrote a couple of years ago to handle invoices, customer contacts, etc (all internally used stuff). Others were complete rewrites (mostly things that hadn't changed in years), a lot of it was originally running on Unix written in Perl. The store-front was originally a Perl script, written in 1995, with many, many enhancements along the way. I probably could have purchased a store-front, but I hate spending time evaluating all possible products to have my choice take me 90% of the way and then I hit a roadblock. One of the main problems I expected with any purchased store-front was the fact that it probably would be difficult to "teach" it about license upgrades. I like my customers to be able to enter their license number and it tells them what the possible upgrades are. Some licenses were sold as bundles or with certain user quantities. Rather than having to become an expert in some store-front, I just decided to roll my own. Credit card processing goes through Verisign which has a nice .NET assembly/web service that can be called from an asp.net application and of course DNN modules like my store-front. Google checkout also offers similar features but I have only looked at it briefly.
The site now handles all the inhouse things (customer contacts, bug tracking, etc.) and allows customers to purchase products, look at their invoices (PDFs generated as needed), download products, maintains their license information (like passwords), keeps track of their product support subscription and nags them to death 
when they don't renew, handles product activation, etc.
Even though the entire development effort took 3 months, it was well worth it. It's a great improvement to the "old" site. DNN brought in so many features like user roles, navigation, tons of free modules and it's a great framework to develop your own applications/modules. The reason it took 3 months is mostly because I didn't know DNN and spent most of the time gathering information (aka Google). The documentation for DNN is a major minus, except that you always have access to the source, which is an invaluable source of information.
Assuming you are just starting out with DNN you should definitely get the new WROX book DotNetNuke 5. DotNetNuke Module Programming is also a worthwhile investment.