Website:
The Web Site project is compiled on the fly. You end up with a lot more DLL files, which can be a pain. It also gives problems when you have pages or controls in one directory that need to reference pages and controls in another directory since the other directory may not be compiled into the code yet. Another problem can be in publishing.
If Visual Studio isn't told to re-use the same names constantly, it will come up with new names for the DLL files generated by pages all the time. That can lead to having several close copies of DLL files containing the same class name,
which will generate plenty of errors. The Web Site project was introduced with Visual Studio 2005, but it has turned out not to be popular.
Web Application:
The Web Application Project was created as an add-in and now exists as part
of SP 1 for Visual Studio 2005. The main differences are the Web Application Project
was designed to work similarly to the Web projects that shipped with Visual Studio 2003. It will compile the application into a single DLL file at build
time. To update the project, it must be recompiled and the DLL file
published for changes to occur.
Another nice feature of the Web Application
project is it's much easier to exclude files from the project view. In the
Web Site project, each file that you exclude is renamed with an excluded
keyword in the filename. In the Web Application Project, the project just
keeps track of which files to include/exclude from the project view without
renaming them, making things much tidier.
Reference
The article ASP.NET 2.0 - Web Site vs Web Application project also gives reasons on why to use one and not the other. Here is an excerpt of it:
- You need to migrate large Visual Studio .NET 2003 applications to VS
2005? use the Web Application project.
- You want to open and edit any directory as a Web project without
creating a project file? use Web Site
project.
- You need to add pre-build and post-build steps during compilation?
use Web Application project.
- You need to build a Web application using multiple Web
projects? use the Web Application project.
- You want to generate one assembly for each page? use the Web Site project.
- You prefer dynamic compilation and working on pages without building
entire site on each page view? use Web
Site project.
- You prefer single-page code model to code-behind model? use Web Site
project.
Web Application Projects versus Web Site Projects (MSDN) explains the differences between the web site and web application projects. Also, it discusses the configuration to be made in Visual Studio.
The company I work for targets Mono on Linux as our main deployment environment. Thus there is no "additional" work - we provide the whole stack, from hardware, through operating system (customized and trimmed) to applications. Using Open Source gives huge savings for us and our clients (and yes, we do contribute back to the OS Projects we rely on).
The important thing is to constantly test using your actual target (sorry, Mono on Windows doesn't count). Sure, developers use Visual Studio, but the continous integration (using CruiseControl.Net, you'll need Mono 2.4.2 to run it on Linux) is done both on Windows and Linux, testing all Mono versions we expect to work on (it got much more stable recently, but still, regressions do happen between releases). It's quite easy to run parallel Mono versions on one *nix system, you can even include an svn snapshot build if you prefer to catch upstream regressions early. If you don't roll out your own distribution, then remember that most Linux vendors ship Mono with custom patches - this has caused problems for us before. Also, many distributions have a lot of lag updating Mono, and this is a rapidly advancing project.
For database layer we use mostly "plain" ADO.NET - Oracle (with dotConnect for Oracle, they support Mono) and SQLite (Mono ships with a working connector). I have also used the official ADO.NET Driver for MySQL (Connector/NET) and it, too, works well. ORM mappings are more tricky, but NHibernate is usable (keep in mind that they do not support Mono officially).
As for the build engine and tests - NAnt and NUnit are well known and well tested. With most recent versions of Mono xbuild (clone of MSBuild) actually got usable, but prepare yourself for contributing quite a lot patches if you decide to use it for more complex scenarios.
Write tests. Lots of them. Be prepared to contribute patches and bugreports, and if you use commercial components - make sure the supplier officially supports Mono.
Best Answer
Check out SharpDevelop. This is the closest you can get to your requirements.