For example, I like running the latest version of Vim (OS X is often behind). Compiling from the source, I can control what the binary is named (to avoid a name collision with the built in Vim), I can control the features (--with-features), and I can have it install to a directory of my choosing (~/Applications, where I also have scrypt install).I also install Lame and FLAC this way.

As for bread, no, I am horrible at cooking!

That's quite wise, particularly regarding the feature selection. Such joy from having the source!

I suppose I never run into this problem because I don't use the software to its full extent and therefore don't miss any features! I must be lazy.