Well not exactly 'different' crypto. But yeah you have a point. You would use the best method (or most secure) of encryption available to you, then why bother with wrapping anymore with anything less secure? Well i guess you wouldn't, you would use the same. But my point is that a method like that wprks purely for a time constraint point of view. Say you are trying to crack a password... at what point will you give up and say "bad luck, i couldn't crack it"? 1 week? 3 months? A year?
If you have a trucrypt volume with say, a 16 character passphrase. Then inside that you have another truecrypt volume (same crypto or not) with a different 20 character passphrase (obviously would have a different hash, was created at a different time), then it WILL make it 'harder' to crack because you have only gotten half way if/once you crack the first container. And how long did that take? Who knows how long the second one will take? Will there be more encrypted containers inside this one?
Obviously if you don't want government agencies getting to your stuff, you have a lot of other things to think about than encryption (yes, they probably already have those files archived off somewhere and have a nice meta search cluster at the ready to find anything on you at any time). But i believe that by having multiple encryptped volumes or containers inside each other, all with different (obviously long, random) pass-phrases, and all created with different hashes, the chance of cracking your way through each one will take longer and longer. Not really practical for every day file use like you state. But if you worked on the files maybe a couple of times a week, having to enter a few different passphrases at different levels may be worth while.
All depends on where you draw the line from security/usability and is it worth while.
--just for fun--
And i guess for tinfoil paranoia fun you could say, have your linux partitions encrypted automaticly, then use an encryption program to do its own full disk encryption, then create a virtual machine on that host. Install an OS with disk encryption. Inside the VM make numerous serpeate encrypted volumes with differernt passphrases, then have your files at the root of it all (inside the containers which are inside the VM). Shut down the VM. Create an encrypted container, move the VM inside that. Then move that container inside a few more containers. Oh and of course, the actual data you are protecting is a stenography file passworded with RAR then residing in a PGP file. Haha i'd actually be curious to see how fucking slow working with that would be :)
--maybe not so fun--