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When a user logs in, environment variables are set from various places. That includes /etc/profile (for all users).
Then all the files in the /etc/profile.d directory.
Then ~/.bash_profile, then ~/.bashrc.
/etc/profile.d/ is a good place to put your application specific setups. For example, I always use SSH for CVS (cf. RSH). So I use:
echo "export CVS_RSH=ssh" >> /etc/profile.d/cvs.sh
chmod +x /etc/profile.d/cvs.sh
See also: http://www.linux-migration.org/ch02s03.html
Check your /etc/profile.d/ script has a .sh extension. Else it looks like the bash shell will not pick it up.
