In the upgrade from 12.10 to 13.04 I lost the ability to use Ubuntu Tweak's Janitor to clean caches so I would like to know how to do it from the command line.
I've never used any such software but if you're talking about caches, I think you might mean downloaded APT packages in /var/cache/apt/archives which are cleaned with sudo apt-get clean.
If you mean package/source package caches, then these can be re-generated with apt-cache gencaches. If you want to remove them for some (odd) reason, they're held in:
/var/cache/apt/pkgcache.bin
/var/cache/apt/srcpkgcache.bin
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