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We're working on a project in which the customer needs the Ubuntu server on which a web app and database are running to be "encrypted at rest". What's the best way to implement this?

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That's highly situational. It seems to me like you're asking about an PCI compliance web-app. The easiest way I've seen this done is mule-ing out the payment details to a payment gateway. Then just handle user identity on the web-app –  hbdgaf Apr 18 '12 at 23:09
    
We have no payments system in the app. It's the application data itself that must be encrypted. –  dan Apr 19 '12 at 1:35
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Sorry but I cant understand what you mean with "encrypted at rest"

if you want to encrypt parts of the system i would recomend lukscrypt and lvm.

http://www.debuntu.org/how-to-encrypted-partitions-over-lvm-with-luks

you will need to have installed LVM when you install the server I would just but the database and the files which you need to keep encrypted on a logical volume in LVM and require manual opening the encrypted partition after each reboot

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Thanks, that seems like a relevant answer. –  dan Apr 19 '12 at 1:42
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