How do I encrypt but share a number of folders?

Question

I want to achieve the following functionality. Is it possible?

• Boot up computer (possibly via WakeOnLan or WakeOnPlan).
• Either be automatically logged in, or log in via login screen, or log in remotely.
  • I change this behavior occasionally, so full disk encryption wouldn't work for me because it requires a password on bootup (which would it would prevent the remote bootup options, and the automatic login option). I am only interested in encrypting data, not the entire harddrive.
• Once logged in either:
  • a launcher/tray icon is available to launch encryption app (preferred)
  • run encryption app from the dash
• Prompted to unlock encrypted folder(s) individually.
• Unlocked folders are available to: me, apps I am running (e.g. editors, SpiderOak)
• Ideally, folders that I share with bindfs can be locked/unlocked by other users too.
• A key point is that once I have unlocked an encrypted folder, I don't want to have to think about it again.

I currently achieve this via TrueCrypt (except for the last part). Unfortunately TrueCrypt isn't well integrated with Ubuntu (licensing issues prevent Debian from including it in their repo, the interface isn't quite integrated with Unity, setting it as a startup app doesn't quite work, sharing encrypted folders isn't really part of its design).

Is there an alternative to TrueCrypt that is better integrated with the Ubuntu GUI and would suit this workflow?