That depends entirely on your source and what you consider a 'word'.
http://wiki.answers.com/Q/What_word_has_two_Q%27s_in_it
This list would suggest there are 28 words with 2 qs, but not all of these are in every English dictionary, and there may be others that aren't included here.
http://www.chambersharrap.co.uk/chambers/books/dictionaries/index.shtml
This dictionary lists 30 different words with 2 qs, which includes only 9 from that other list (equivoque, quaquaversal, quinquagesima, quinquefarious, quinquefoliate, quinquennial, quinquennium, quinquereme, quinquivalent). Some of the others are simply words that weren't included in that list, but most are derivatives, alternate forms, foreign expressions that are extensively used in English, and abbreviations.
These include:
chiquichiqui, quaquaversally, quinqu-, quinque-, quinquagesimal, quinquecostate, quinquenniad, quinquennially, quinquevalence, quinquevalent, qaimaqam, quaquaversal, quaquaversally, quinquagenarian, quinquagenary, ex quocunque capite, quelque chose, tu quoque, qq (quartos), qqv or qq.v. (used instead of ‘qv’)
