When you mark a word, the relevance scores of all other words are re-calculated based on how similar they are to the marked word. This can be very useful for finding other related words or phrases, just sort all words by relevance so you can see which ones are "close" to your marked word.
In addition, marked words can be used to both find relevant results (mark an interesting word or phrase and sort results by relevance) and in executing new searches (mark the words and phrases you want to search on and click the Search button, or right-click a word/phrase and choose Quick Search).
Related Topics:
About the Index
Finding Relevant Results
Iterative Search with Marked Words