It would be unfair not to include at least one South American side in this list, and there is no more deserving team than Boca Juniors.
In the eight-year period from 2000 to 2008, Club Atlético Boca Juniors captured a total of 16 titles, of which five were local and 11 were international. Boca was selected as the greatest South American team of the first decade of the century.
In the second half of 2000, Boca won the local tournament for the first time in two years. Exactly three years later they repeated by taking the "Apertura" 2003 championship. In the 2005-06 season, they took both titles. They went on to repeat as Argentine champions in the second half of 2008.
Boca, however, was much more impressive at the international level during that time period.
Its 11 international titles represent four Copa Libertadores, South America’s equivalent of the Champions League; two Copa Sudamericana; three Recopa Sudamericana, which is South America’s Super Cup; and two Intercontinental Cups.
Boca won the four Libertadores in a seven-year period, raising the trophy in 2000, 2001, 2003 and 2007.
The Argentine squad’s most memorable matches of the current century, however, came in the Intercontinental Cups it captured in 2000 and 2003.
In the 2000 Intercontinental Cup, Boca took on Real Madrid, arriving as huge underdogs but pulling off a gritty 2-1 win. Three years later, and two years after suffering a heart-breaking overtime defeat to F.C. Bayern Munich, Boca hoisted the trophy for the third time, defeating A.C. Milan in the penalty kicks.
Since 2008, Boca has added another national tournament and a Copa Argentina to its trophy case, but the time period of 2000-2008 remains its most dominant in the current century, when the "Xeneizes" ruled South America.