I recently started using apt-cyg and like it a lot. It allows easy installation of packages from Cygwin and Cygwin ports repositories.
It is inspired by Debian’s apt but it does not support anything like a sources.list and it can actually only work against one repo (mirror) at a time. Well, I guess that’s bearable since there are really only two sources (main cygwin and cygwin ports). But I might try apt-cyg-multi which claims to have added the missing cross-repository functionality.
For now, I found it convenient to configure these bash aliases (use a suitable Cygwin mirror and Cygwin Ports mirror for your location):
alias cyg='apt-cyg -m http://mirrors.kernel.org/sources.redhat.com/cygwin/'
alias cyp='apt-cyg -m http://mirrors.kernel.org/sources.redhat.com/cygwinports/'
Update, June 2013: There is a promising-looking apt-cyg fork on github. I just started using it.