[Sanddancer]

Have you taken a look any at the FreeBSD ports system? It uses makefiles to manage pretty much any software install you can think of. Additionally, there's a pretty good infrastructure there for managing custom build trees, etc. Additionally, they also have things like BSDpan that let you use arbitrary Perl modules with the package management system.

[sanderjd]

I've used ports, but I've never developed a project using it, so maybe I should try that out. But "uses makefiles" does not make me particularly optimistic for its pleasantness. I really prefer (and think it's been proven possible to build) declarative, rather than imperative, systems for managing dependencies.