From what I can tell, it only shows apps that are ACTIVELY using system resources. Otherwise, it doesn't bother, as they don't affect the system.
If the app is running like it should (IE: When you're totally done with it, it goes bye bye) it won't show up in the JI6 Task manager, because it's really NOT using anything. (A small "image" of it may reside in memory for quick-launch purposes, similar to a Hybernate mode on Windows OS', but it's not actively "running", and those may show up in other task managers)
Media players, Maps, and Browsers will usually show up because you may have swapped apps, but are not finished with them, and thus are actively still using them (IE: Still playing a song, still on a website, still running Navigation, etc)
Again, this is just from observation.