If you're compiling a software package because you need a particular version (e.g. the latest), then it requires a little bit more maintenance than using a package manager like dpkg. Software that you compile yourself should not go into /usr, it should go into your home directory. This is part of being a software developer.

One way of doing this is to install everything into $HOME/local/$PACKAGE. Here is how I install node on my machine:

./configure --prefix=$HOME/local/node-v0.4.5 && make install

To have my paths automatically set I put this inside my $HOME/.zshrc:

PATH="$HOME/local/bin:/opt/local/bin:/usr/bin:/sbin:/bin"
LD_LIBRARY_PATH="/opt/local/lib:/usr/local/lib:/usr/lib"
for i in $HOME/local/*; do
  [ -d $i/bin ] && PATH="${i}/bin:${PATH}"
  [ -d $i/sbin ] && PATH="${i}/sbin:${PATH}"
  [ -d $i/include ] && CPATH="${i}/include:${CPATH}"
  [ -d $i/lib ] && LD_LIBRARY_PATH="${i}/lib:${LD_LIBRARY_PATH}"
  [ -d $i/lib/pkgconfig ] && PKG_CONFIG_PATH="${i}/lib/pkgconfig:${PKG_CONFIG_PATH}"
  [ -d $i/share/man ] && MANPATH="${i}/share/man:${MANPATH}"
done

Node is under sufficiently rapid development that everyone should be compiling it themselves. A corollary of this is that npm (which should be installed alongside Node) does not require root to install packages.

CPAN and RubyGems have blurred the lines between development tools and system package managers. With npm we wish to draw a clear line: it is not a system package manager. It is not for installing firefox or ffmpeg or OpenSSL; it is for rapidly downloading, building, and setting up Node packages. npm is a development tool. When a program written in Node becomes sufficiently mature it should be distributed as a tarball, .deb, .rpm, or other package system. It should not be distributed to end users with npm.