FreedomCP, my company, can fulfill most of these needs for you right now.
Here's a high-level overview of what we have right now:
- one, central web interface for all of your servers,
- a safe and secure web interface,
- uses a small Python agent to avoid hogging resources,
- avoids clobbering popular default packages (nginx, php),
- creation and management of Python 2.7, 3.3, and PHP 5.4 apps,
- creation and management of MySQL databases,
- creation and management of system users, and
- it is free.

We exclusively support Ubuntu servers right now.
The way this works is that you (1) have a pre-existing Ubuntu server, (2) sign up for FreedomCP for free, (3) get an api key for your server, and (4) install our agent.
Once installed, our agent keeps a low profile and waits for management work to do. (You create work by creating/updating/deleting sysusers, apps, databases in our web interface.)
After having to deal with many control panels ourselves, here are a few reasons I'm very-enthusiastic of our agent-based system.
- No resources on your server are used except for management tasks and basic communication (e.g. "let's see if there's any work for me to do..").
- Our agent connects to us so we can help you manage Ubuntu servers whether they're on EC2, your home network, in a VM or colocated. (If you're a developer, this can help you achieve dev/prod parity.)
- Our agent doesn't expose any public services/ports for FreedomCP.
To be clear, we do not have the following:
- management for email,
- an open source product (though the Python agent is unobfuscated), or
- an installer that's available in the official repos (all other packages we install are signed and managed by apt).
We're new, but we're just getting started :)