I know of the following:
- The venerable
getopt(3) - The extended
getopt_long - glibc's
argpparser for Unix-style argument vectors - popt from the GNOME project (or its spiritual successor in Glib)
I'm sure there's more that I haven't used or even heard of; a quick Google search reveals Gopt, argtable, and Optlist.
Personally, I like argp best, and every program I wrote using getopt/getopt_long (beyond a certain baseline of complexity) has been converted to use argp. It's more widely available than popt, more powerful than getopt_long, well-documented, consistent with all the GNU-style conventions, and very flexible. On the downside, it's far from the easiest to use (thanks to being so flexible), and the code to support it is quite verbose (as are many things in C).
What do you use, and why?
Yes, I mean C rather than C++. There are a ton of C++ parsers, but I don't use C++.
John Millikin notes that popt is no longer maintained. I list it because many programs still use it -- including AbiWord, rpm, rsync, and samba -- despite Gnome's efforts to migrate away. But I've added a link to Glib's argument parser now, too.
For C++ argument parsing, see the question c command-line parsing