Despite their best efforts, search engine spiders aren’t human. As such there are some things you should be aware of that work fine for humans but make your site difficult for spiders to search:
Flash navigation: If the links on your web site are made of Flash animation, it’s hard for spiders to follow the links. Search engines will eventually be able to navigate a Flash site, but for now it’s difficult for them.
Password protected pages: All of the advanced tutorials on my password protected web site can’t be searched because spiders don’t have a username and a password to get to the content. So that content on my web site will never be searched by the search engines (until that fine day arrives that Google trains their spiders to open a PayPal account and pay me money each month) (that’s unlikely).
External scripts: Sometimes the links of your site are created using external scripts. Some advanced navigation, like drop-down menus, use external files that make it hard for spiders to follow.
(if that previous line made any sense to you whatsoever, you’re a bigger nerd than I am)
Frames: Frames are a way of displaying two html files on one page. They were used a lot to let you scroll around a page while keeping the site navigation in one spot. An older way of creating a web site, frames still have their uses but spiders have a hard time indexing them properly.
The next step is to learn how to make your web site very attractive to search engines (both by what you do on your web site and off).