Make sure you don't use color alone to label content areas, convey meaning, or give directions to users. Color deficient users may have problems seeing the colors you're using to convey meaning with. So, I recommend that you always use text to assist color deficient users.
Color is, however, an important part of life for most people, so while you can use a variety of colors on your site, don't cluster sensitive colors (say, red and green) right next to each other, or demand that colors be used as one of the main navigational tools.
Always provide clear textual options... some people still have monochrome monitors!