I am working with a company who has built a custom eCommerce web application in .NET and they want to have the main site be built on Wordpress. Is this possible to have a wrapper on a site that is in wordpress and build pages to display .NET coding?
Is it necessary to have wordpress and .NET on the same site? Those are two completely different things and my recommendation would be to not mix them together. You might create main site on e.x. www.mydomain.com, and ecommerce on a subdomain: shop.mydomain.com.
as Spart said your talking .NET (microsoft) v's PHP ... for a hack try integrating the store into the WP site architecture / pages via iFrame(s) ... or if as u say it's a custom .net store (in house dev i'm assuming) jsut get their dev to add a JASON interface to the store system and pull it into WP / PHP that way ...
Well, iFrames are a really bad practice and may cause lots of issues. One thing is to embed an image or video via iFrame, but definitely not the whole application. On the other hand, this idea with JSON is not that bad. Implement API/webservices on eCommerce application and refer to them from the wordpress template/page/where-ever.
I would not use iframes. As mentioned - bad practice IMO. The only issue with having a subdomain with the ecommerce is we would need a "cart" on all pages including wp pages. So that is a conflict of code language. Really this is the only hurdle we have.