Developing with SharePoint (both MOSS 2007 and SharePoint 2010) I've encountered a rather big problem: even if you deploy a wsp to a single web application (how to achieve this is described in the post SharePoint: how make your wsp deployable in a single web application ), your features are visible to every web applicaton in the farm.
This same problem has already been discussed in the page Is it possible to deploy a solution to a web
application so that its features are only visible within this web application? and in the blog post comment that sais: There is a disconnect in SharePoint where while Solutions are deployed to Web applications, Features are installed on Servers (but read the entire article because it is very intresting).
Worse, if you have automatically activated farm and web application features, they activate even in web applications where your wsp is not deployed! So the rule is: always disable auto activation of farm and web application features, like described in the article Do you turn off auto activation on farm and web application scope features?