Your question was tagged with ASP.NET, but I didn't see any ASP.NET specific stuff in your question. Pluggable ASP.NET is possible, but hard using System.AddIn, aka MAF. I managed to create a secure web-site plug proof of concept in in about 4 days.
http://suburbandestiny.com/Tech/?p=585
http://suburbandestiny.com/Tech/?p=588
The cool thing was finally being able to run an Add-In dll in Minimum Trust, while the host app ran in full or medium trust.
I finally concluded that System.AddIn was created to solve the AddIn challenges faced by Microsoft Office, not the challenges of creating an AddIn for a web.app.
MEF is supposed to be the new shiny thing to do add-in type patterns, but I don't have any experience with it. MEF was meant to be a general solution and not just to solve problems on the MS Office team, so it is somewhat more promising.