I saw some work being done on this area and I thought I'd share some feedback around it, with regards to things that annoy me currently.
Having "Show More Applications" hide and show the Utilities / Developer Tools is reasonably annoying. I think it'd be much better to have Show More Applications just directly link to something like in D9297.
The other thing is that I often find I have to configure the applications shown before it's useful to me. Since everyone in an organisation using Phabricator is going to be using different parts of the system, having to configure the applications shown on the left hand side is annoying.
I think that a heuristic based on "what has the user visited / used recently" is probably a much better idea, with a pinning system. This is how the Windows Start Menu works (in Windows 7) and it works brilliantly. I don't have to configure it to tell it what I use often, and if there's a tool that I use infrequently (or most commonly, have just installed) but I still want it within arms reach it's only a click away to pin it to the top.