The best way to fix the color problem is to set your term type to putty instead of xterm. xterm is black on white by default, so you'll get ls colors and vim syntax highlighting more suitable for a light background.

If you want to change individual colors, try setting the LS_COLORS environment variable, or in Vim you can try running ":color blue", ":color evening", ":color ron", or any other color scheme name under the /usr/share/vim/vimversion/colors directory.

Also note that PuTTY doesn't work well with the Consolas font and bold text, since the bold text is larger than the normal text. Lucida Console, Andale Mono, or Bitstream Vera Sans Mono are all really nice.