If the variable in question is PERL5LIB, you can also add paths by right-clicking the project, choosing Perl Include Path, and adding ${project_loc}/lib or whatever.
I have already put the appropriate export statements in the .profile shell-script...
Then one would conclude that .profile isn't getting executed. Perhaps you are using a GUI? For KDE, I created the following shortcut:
$ dir .kde/env/
total 0
lrwxrwxrwx 1 eric users 24 Jan 20 2009 profile.sh -> /home/eric/.bash
+_profile
$ cat .bash_profile
...
export PATH=~/usr/perlbrew/bin:~/usr/perlbrew/perls/current/bin:$PATH
export PERLBREW_ROOT=~/usr/perlbrew
...
Surely there's something similar for OS/X.
This way, you can solve the problem for all applications, not just Eclipse.