Hold on, you need to do some research before you take out stopwords (aka noise words, junk words). Index size and processing resources aren't the only issues. A lot depends on whether end-users will be typing queries, or you will be working with long automated queries.
All search log analysis shows that people tend to type one to three words per query. When that's all a search has to work with, we can't afford to lose anything. For example, a collection might have the word "copyright" on many documents -- making it very common -- but if there's no word in the index, it's impossible to do exact phrase searches or proximity relevance ranking. In addition, there are perfectly legitimate reasons to search for the most common words: people may be looking for "The Who", or worse, "The The".
So while there are technical issues to consider, and taking out stopwords is one solution, it may not be the right solution for the overall problem that you are trying to solve.