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In the case of a rooted phone, what are the various options to stay anonymous and keep your data secure? I've seen the guys at The Guardian Project work towards this: https://guardianproject.info/apps/

And Whisper Systems: http://www.whispersys.com/

Is there any means to individually protect each application with a password or encryption? Say you want your Image Gallery, SMS / Whatsapp inbox to be encrypted or accessible only by a password instead of a single device password.

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not an answer, consider it a joke: paranoiacs must not keep any sensitive data on android –  Vitaly Nikolaev Dec 20 '11 at 22:26
    
please accept some answers to your questions –  Lohoris Jan 20 '12 at 9:04
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up vote 1 down vote accepted

You should look for open source solutions whenever possible since closed source solutions aren't subject to as much inspection. Apparently the Guardian Project's links passed this test.

If you want anonymous web browsing, then you probably want Tor, which the Guardian Project lists. Off-the-Record works quite well for encrypted IMs, but it's vulnerable to traffic analysis.

The Guardian Project recommends the full disk encryption program LUKS, which sounds good. You can however protect specific directories under Linux and BSD (Mac OS X) using EncFS's mount-on-demand mode and an external password prompt program.

encfs -idle=30 --ondemand --extpass='.../ssh-askpass' ~/.private.encfs ~/.private

In theory, you'd see an ssh password prompt if any application attempted to access any file inside that directory, assuming 30 min had elapsed since you'd last accessed it.

This will not work if an application attempts to access the data too frequently because encfs will never reach the idle timeout. Ergo, you might need to play around with exactly what applications support such operation.

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