Even though OS X includes a handy contextual menu for zipping and unzipping files, the decompression chores (handled by the BOMArchiveHelper.app tool, originally built for expanding components during software installs) aren't always managed as cleanly as one might like. The default behavior of the expander is to leave the original files intact after processing, leading to a phenomenon termed "zip litter" by a colleague. Blech.
If you're seeking a zipless desktop, check out The Unarchiver by Dag Ågren, just updated to version 1.6. Built from the bones of an ancient Amiga decompression library, this Swiss Army knife can handle almost any format you can think of and probably a few you can't -- I'm personally very excited to crack open some DiskDoubler files that have been languishing on my old Bernoulli media. With the exception of the proprietary SITX archives, where you'll still need an instance of Stuffit Expander, this free tool can handle everything else.