Fortunately, this is configurable with the LSCOLORS environment variable. The default string is "exfxcxdxbxegedabagacad" for OS X. However, on Linux, it looks more like you may be able to configure this using /etc/DIR_COLORS instead.
On my CentOS 5.4 machines, DIR_COLORS lists the entry for directories as "DIR 01;34", which means that it uses a bold blue on the default background. One option to ensure a bit more contrast would be to change this to always print on a white background. So you would change this entry to look like:
DIR 01;34;47 # NEW default is Bold blue with White background
References:
change ls colour (color) in bash - GlowingApple explains back in 2005 how to change colors on the MacOSXHints forum
COLORS Lscolors - another page that explains the LSCOLORS variable
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