A page in the Beyond Linux from Scratch manual describes environment variables that should be set when installing software in a non-traditional location (e.g. your home directory).
I've written a sh/bash include that can be included from .bashrc to set these variables, as well as PYTHON_PATH for separately installed Python libraries:
#!/bin/bash
PREFIX=$HOME/usr
export PATH="$PREFIX/bin:$PATH"
export PYTHONPATH="$PREFIX/lib/python2.4/site-packages:$PYTHON_PATH"
export MANPATH="$PREFIX/man:$MANPATH"
export INFOPATH="$PREFIX/info:$INFOPATH"
export LD_LIBRARY_PATH="$PREFIX/lib:$LD_LIBRARY_PATH"
export PKG_CONFIG_PATH="$PREFIX/lib/pkgconfig:$PKG_CONFIG_PATH"
export CPPFLAGS="-I$PREFIX/includes $CPPFLAGS"
export LDFLAGS="-L$PREFIX/lib $LDFLAGS"