I've read recently some criticism (see 1, 2, 3) about the packaging distribution system of two popular programming languages: Ruby gems and Python eggs. The most important argument stated against them is that they replace the system package manager (in case there is one, as in every Linux distribution), which makes eggs and gems difficult to track, code difficult to patch, and so on.
Are actually eggs and gems right? In case not, are there any alternatives to distributing Python or Ruby modules? Should developers focus on taking advantage of package manager (apt-get, pacman, ...) capabilities?