Have you ever noticed this couple of small but very useful features in Team Foundation Server and Visual Studio Team Services?
You can query across projects – think about it, you can create a cross-project (in case you are not using the One Team Project approach) query which can be pinned in the main dashboard. A very minor thing bringing a lot of value to certain roles.
You can compare different fields! I realised this a few days ago (my bad!), and I think it dramatically improves the custom queries’ experience, given that you can build a result based on field comparison.