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@Velocio
The stop word list is built into MySQL. It's part of the database product itself and the software needs to be re-compiled to make it do anything other than the binary releases... re-compiling isn't a good idea as it breaks updates and basically means that if a security flaw is found then I'd become responsible for packaging it rather than just using the binary packages provided by MySQL.
The full stop-word list can be found here:
http://dev.mysql.com/doc/refman/5.5/en/fulltext-stopwords.html
There's not a great deal that can be done about them though... except to use tagging as a workaround for anything that is too short to search meaningfully for, or for anything on the stop word list. The tagging works where the normal search doesn't as it's a separate and self-contained search index that has been hacked onto the forum, and it doesn't use MySQL to do the heavy lifting of performing a search (since tags are simplistic and don't require phrase based searches or the ability to handle minor mis-spellings).