Web Application Scoped Resources
When you try to deploy a solution without Web Application Scoped Resources, you will get the following errors:
The solution contains no Web application scoped resource, and therefore cannot be deployed to a particular Web application. It can only be deployed globally.
If you like to deploy the solution to a web application, you need to set the Assembly Deployment Target to WebApplication instead of GlobalAssemblyCache. You can download a deployment script here.
A web scoped solution will contain files, features, and assemblies etc that are deployed to specific web applications (or All of them as selected). If there is an assembly destined for the bin directory or a feature set as WebApplication, Site or Web Scoped, then the solution deployment screen will ask you which web application to deploy the solution too (there are other triggers, e.g. App Resource Files (.resx) etc). Of course though, you may have globally deployable files in the solution (e.g. GAC located assemblies) as well as web app scoped resources.
When deploying web app scoped resources, any modifications to the bin folder, app_* folders, web.config etc will only apply to the web apps the solution has been deployed to (or all of them if selected – this option does not include Central Admin or the SSP web app!). Any newly created web apps will not receive these changes UNLESS you have also deployed files into the LAYOUTS/* folder(s) which get merged during web app creation (this is a separate topic all together).
Globally deployed resources are available to ALL web applications on the server, these tend to include farm scoped features, GAC located assemblies and files being deployed into the LAYOUTS/* folder(s).
The difference between deploying “globally” and to all content web apps depends on what you are deploying. If there are web.config changes or web application / site / web scoped features, then these cannot be deployed globally anyway – the option will not be displayed as they must be deployed to a target web application(s).