I am using the most excellent MacFamilyTree 7, which is the program for creating, managing and publishing of family trees. IMHO, that is the ultimate tool for the job. Mac Family Tree will automatically build an entire web site for you. You can then export it to a folder and easily integrate with your main web site (I use NimbleHost’s Hijax for integration).
After publishing, all the necessary navigation is already built-in. You can find a wealth of information about single persons, entire families, dates, places, statistics, etc. Viewers can download the zipped file containing the entire tree to their computers. If you need to password-protect the tree, you can use any one of several RW stacks for password protection.
Here is a screenshot of the site I created this way:
