I've run Bamboo on both Windows 2008 & Ubuntu, and I prefer a clean Ubuntu server install over Windows, no contest. Stability, performance, etc. While Atlassian seems to support virtually all major OS's, they seem to lean towards using Linux to host, and of all the flavors of Linux, Ubuntu seems to be the "most" supported, as it also appears to be the most widely used Linux server install by their userbase.
Since Jira is our "flagship" Atlassian app I have it on an Ubuntu 12.04.2 LTS server with an external db server, Bamboo I have on a 13.04 server that I keep updated (not LTS) with an external DB server as well. (same db server actually, for both Jira & Bamboo).
I've had no issues with the install or performance. (no local agents either - just remote). I'm very satisified with our OS choice.
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