Frames are very problematic. search engines cant read them. They read only the first frame and don't continue to the rest.
Flash pages - if they are built only as flash and don't have extra content can cause a problem. Flash elements on regular pages are OK.
dynamic links - java, ajax etc. search engines can't follow them and cant index the pages they refer to.
There are many more elements, but the best way to find out how a search engine sees your site is to use a search engine spider simulator. There are many free ones on the net (some of them come as toolbars).
Here is a link to one of them:
search engine spider simulator