My favourite archive tool in Debian is "unar", which will take just about any archive format, and intelligently extract it into a subdirectory (if the archive has everything inside one parent directory, it uses that, otherwise it makes a new directory and puts everything in there).

Unfortunately, it's based on an OS X tool, which means it needs the GNUStep runtime, which makes it a pain in the neck to build unless your Linux distro has already done the hard work of packaging it for you.

I've also heard good reports about bsdtar handling many archive formats intelligently, but I've never actually tried it myself.