The present system, brought in by the Treaty of Nice, uses a complicated system where countries had a certain number of votes - that benefitted the small countries, and disadvantaged the large ones. For instance, Poland and Spain, which each have about half of the population of Germany, each get 27 votes, compared to Germany's 29. The constitution says that for a resolution to pass, it must be passed by both (a) 55% of the member states, and (b) states representing 65% of the EU population. (a) means that small states can't just be ignored by the large ones, and (b) is democratic.
See
http://news.bbc.co.uk/1/hi/world/europe/3562405.stm(note that the BBC link talks about the draft constitution proposal, which was 50% of the states, and 60% of the population).