Just before Christmas I worked on a couple of projects where we needed to have Umbraco running in a virtual directory. Out of the box, Umbraco itself works very well in a virtual directory these days. The main issue that I ran into was packages that didn't work correctly when Umbrco was in a virtual folder.
From going through all the affected packages in the projects, I've compiled a list of things that you can do in your packages to help ensure that it will run correctly when your site is running in a virtual folder. So without further ado, here are the top five things to be aware of:
1. Paths in your package manifest
In your package manifest, ensure that your paths start with a ~. E.g. instead of referencing a script as "/app_plugins/my_plugin/script.js" use "~/app_plugins/my_plugin/script.js". Umbraco will then work out the correct path when it loads in all of the manifests.
2. Paths in your CSS
You often see people make their image paths in the CSS relative to the root of the site. This won't work in a virtual folder, so make sure all of your image paths are relative to the location of your CSS file. That way the paths will work, regardless of where the Umbraco site lives.
3. Paths in your JS
Again, it's common to see links to things in the JS file be rleative to the root, e.g. "/umbraco/surface/mysurface/get". Your JS will be executing from the /umbraco/ path, so code your paths accordingly. E.g. in the previous example, you could use "../umbraco/surface/mysurface/get".
4. Paths in your templates
As with paths in your JS, code the paths to images and other resources in your templates/views as if they're in the /umbraco/ folder. So instead of "/app_plugins/myplugin/images/", use "../app_plugins/myplugin/images/".
5. Paths inside your code
If you're mapping paths inside your code for things like Controllers and other compiled resources, don't forget the ~ at the start of the URL! this will then map the path to include the virtual folder as well.
And that's about it. If you follow those five guidelines, your package should work on an Umbrco site that's running in a virtual folder!