How to effectively implement sitewide file encryption?

Pig Hogger writes: The recent assertion that, given the recent CIA/Wikileaks dump about “encryption really working” makes encryption much more desirable.

So, if you decide to implement server-level encryption accross all your servers, how do you manage the necessary keys/passwords/passphrases to insure that you both have maximum uptime (you can access your data if you need to reboot your servers), yet that the keys cannot be compromised, as if the password is known by many different people, because, once the server is seized, you can’t change the password?

What are established practices to address this issue?