I have used a standard set of milestones which had to be applied to each project and then an external spreadsheet to collate across the programme. We had (from memory) 6 milestones picking up key points such as Started, Business Case complete, Initiation complete, Ready for testing, UAT complete, Implemented. In excel we than could weight them by size of project and different "scores" for each milestone which then allowed a very crude form of earned value when comparing baseline to current plan etc.
To do this I had a field for milestone reference which output a table with ID | name | milestone ID | % complete | project and used this data to produce the curves and % complete etc.