Plus most of these tools are geared towards the structured initial development phase, and become considerably less usable once a product is live and goes into maintenance mode. This is odd, since the major part of a projects lifespan consists of maintenance, not development.
The one great missing online tool IMO is one that both integrates and separates the way the user experiences issues (like via Zendesk) and the way those issues are split up, prioritized and handled by developers (any known issue tracking system like Redmine etc).
Right now, every team I know either uses two systems in which the relationship is handled manually (and thus labor intensive and prone to errors) or one system that is only geared towards either audience.
But I do wish more support systems worked this way.
WIP limits and ordered backlogs are missing. There is no need to make 'custom views' for a whiteboard - with Jira they are like 5 different ways to get to a list of items that need to be worked on and I'm never quite sure I'm looking at the right list.
Either way, I work from South America for clients in the US, so I like having these tools around. Specially when they innovate in any way. That means better tooling for communicating with my clients, which is the #1 problem of distributed teams :)