@Craig Hyatt - as one recent example, on a site running the Adv Agg module (advanced aggregation and minimization) and the JQ Multi (allows you to run different versions of JQuery b/c this is a D6 site that the client wanted themed using Bootstrap), the Adv Agg module stops JQMulti from doing it's magic (the libraries don't get included at all), so anything depending on it dies. It works fine with no aggregation or the in-built aggregation.

We also found that Adv Agg killed the Rubik admin theme functionality. So though you get some nice features with Adv Agg over standard aggregation, it wasn't enough to warrant the hassles.