we have quite a lot of services and webs that we wish to be able to deploy separately. We also wish to set up bundles that deploy many of these at once. We have setup the bundles and it works like a charm. What we had to wait with is setting up all individual services and webs because it quickly became hard to get a good overview of the projects.

Take a peek at teamcity and their way of managing projects and see if there might be some improvements on this area.

Source: http://help.octopusdeploy.com/discussions/problems/21785