Stop words are words that the search engine filters out before processing as they are not relevant to the meaning of the phrase.
Common words that are filtered out include common, short function words such as:
a, an, and, are, as, at, be, by, for, from, has, he, in, is, it, its, of, on, that, the, to, was, were, what, will, with, etc.
For example, a search for:
'What are Manchester United's fixtures for this season?'
would be likely to be processed by the search engine as:
'Manchester United fixtures this season'.
However, there is no consensus among natural language processors as to which words are stop words and which aren't. Check out Ranks NL's comprehensive list for a thorough example of how many words can be considered stop words.
If a stop word is relevant to the phrase it won't be filtered out. For example, filtering out the 'the' in a search for the TV programme 'the office' will not return the same results as a search for 'office':