I recently moved from MediaTemple's Legacy (dv) 4.0 VPS server to their new Self Managed DV server. You get to save up some money at the expense of all the software that comes pre installed on a server. All you get when you rent one of these badboys is an empty box with your choice of OS. Sounds exciting!? You bet your ass it does! It can also be a bitch if you're not as familiar with how things work in a web server. Getting this setup helped me understand servers unlike never before and having full control over everything that happens in your box does feel kinda nice.
The best free application I found for managing websites is Webmin + VirtualMin. Though I would like to mention Ajenti, which looks pretty badass and seems to be in active development.
I come from Plesk which was definitely a superior tool but so far I envy noth