MacOS – bzip2 compression library not found error

I think it depends on how many tools/libraries you need to install.

If just git then use Xcode 4 which you will need for any port package. If you are doing pure HTML/Javascripy/CSS then the git installer will work.

For python and perl and similar interpreters the the language install tools can be used unless there are complex C/C++ libraries

If only a few others then build into /usr/local

However if you have several things to install or there are complex dependencies then I would use a ports package like Fink, macports or homebrew (which is best is debatable and should be a separate discussion)

Take the path that you used for --prefix= during your ./configure and sym-link that into the Cellar/ directory that Homebrew is using. Homebrew will see these directories and see the dependencies as satisfied (unless you need to have them compiled with or without certain features to make Homebrew's formulas compile correctly). If your manually-compiled deps aren't compiled correctly, you'll probably get errors out of Homebrew.

ln -s /path/from/prefix/ /usr/local/Cellar/path/from/prefix

(Note the trailing slash on the first path, and lack of trailing slash on the second. OS X can be picky about these slashes when creating sym-links.)

This is the wrong way to do it, you should just be using --ignore-dependencies coq — that's what it's there for.