Search engines do not list every page on the Web, a fact that has become well publicized over the past two years. But by making some architectural changes, you can increase the odds that more of your pages will get listed. If you use frames, get rid of them. Frames put up a serious roadblock to many search engine crawlers. If you did nothing else, your search engine-related traffic will increase because more of your pages would get listed.
Large sites face another problem.
In general, search engines gather a sample of pages from each site they visit. They don't do a deep crawl and list every page. This means that if you have multiple Web sites, you'll probably get more pages represented than if they are all within one single site. Although these are distinct sections, they still reside within the main university.edu Web site, and a search engine will typically sample only a certain number of pages from within that entire site. This is no longer the case.