How to know what packages are available with (home)brew

Definitely Homebrew. I started with Fink, then switched to MacPorts (happier), then Homebrew (much, much happier). These are my reasons for using each (a pro list if you will):

Fink

• Apt-based - feel right at home if you come from a Debian-based environment

MacPorts

• Unlike homebrew do not depend on MacOS library that may change in the future.
• Install everything in /opt/local
• Nice variants system that lets you customise the build
• Easy and intuitive port files, also allows you to add your own
• supports many versions of OSX and macos going back to Tiger including PowerPC versions see other answer

Homebrew

• Maximum leveraging of what comes with OS X. Unlike Fink or MacPorts, it does not require you to build/install ruby and libraries from scratch just to install some small Ruby-based tool.
• Installs into /usr/local
• Install without root access
• Every installed package is cleanly sandboxed into its own cellar so you don't have stray files all over your system, just symlinks from bin, man, etc.
• Has guides and automation to create your own formula files (ie. package descriptors)
• Written in ruby and all formulas are concise ruby scripts

pkgin

• Everything installed in /opt/pkg/
• backed by pkgsrc community and Joyent
• Known to work on NetBSD, DragonFly BSD, Solaris, Debian, Mac OS X, Minix

https://pkgsrc.joyent.com/install-on-osx/

http://pkgin.net/

I think that a package manager will do most of what you need. I will show macports as that is the one I know but the others have similar functionality.

If you use the standard packages ie the up to date ones that have been packaged then macports will do all the dependencies for you. e.g. building scipy knows it has to build numpy first and will do it. You can also ninstall a port easily - macports will tell you if any ports depend on it. If a port is chnaged then macports will update the ports depending on it.

You can also manually chnage the port to deal with development versions of numpy for example. You will have to produce a copy of the port file and edit that see macports guide. The minimum would be to change the version and the rules for downloading so you get different code but can include many patches for OSX specific functions.

You can keep track of what you have installed by port list (also more advanced calls to minimise the number of commands you need. The changes you made will be in your local Portfile repository which will need to be backed up and a small change to the defualt macports config made.