Like many people, we're currently using Jira over HTTPS. This means (as you guys have already blogged) that all JS files are loaded sequentially and not cached. The vast majority of JS files referenced are in the <head> of the page, which means it can't even start to render the body until they're all loaded. This is particularly bad for us because not only are we using a remotely-hosted Jira (and so each JS file load seems to take at least 100ms, often much more) but we've installed the Jira Labels plugin, which adds 10-15 more JS files to most pages. Hence, 12 seconds before render.
Ideally, everything should work fine after this. Unfortunately, it's not always the case - several parts of the page template use inline JS which execute as soon as they're loaded. In some cases, e.g. the auto-completing user picker, the code is referencing YUI functions which haven't been loaded yet. What the code should be doing is deferring until the page is either fully loaded (by onLoad) or, even better, the DOM is ready (see: http://dean.edwards.name/weblog/2005/09/busted/ and follow-ons).
The speed of Jira is a major issue for us (Linden Lab); making these tweaks would be of significant value.