[2] Papaloukas helped lead the Greece men's national basketball team to a title, EuroBasket 2005, and a silver medal in 2006 FIBA World Championship.

In 2001, Papaloukas finally moved to Olympiacos, a long-time Greek League power, as well as one of the perennial contenders in the EuroLeague.

After the 2001–02 season, he left Olympiacos, and moved to another EuroLeague powerhouse, the Russian Super League A club CSKA Moscow, in 2002.

After three disappointing years, at the club level, Papaloukas was a main factor helping the team win the 2005–06 EuroLeague title, the club's first EuroLeague title in 35 years, with a clutch performance in the 2006 Final Four - 19 points in the semifinal against FC Barcelona, and another 18 points at the final against the then back-to-back European champions, Maccabi Tel Aviv, which led to him being awarded him the Final Four MVP award; after he was also named the best point guard of the EuroLeague for that season.

[4] Alongside him on the All-EuroLeague First Team, were the best shooting guard, Juan Carlos Navarro of Barça, the best small forward, Anthony Parker of Maccabi (the 2005–06 EuroLeague MVP), the best power forward, Luis Scola of TAU Cerámica, and the best center, Nikola Vujčić of Maccabi.

Papaloukas scored 23 points and dished out 8 assists, but a number of sportswriters intimated that he did not receive adequate support from his CSKA teammates, and thus his team lost the final.

Papaloukas was then pursued in free agency by the NBA clubs the Boston Celtics, Los Angeles Lakers, Milwaukee Bucks, and the Miami Heat to fill their point guard spot.

However, on 7 July 2007 Greek newspapers reported that Papaloukas agreed to a newly structured 3-year contract with CSKA, worth €10.5 million net income.

On 13 August 2011 Papaloukas signed a contract with the Israeli team Maccabi Tel Aviv, the finalists of the 2010–11 EuroLeague.

He was signed by the team, and then officially returned to the court in a EuroLeague game against Anadolu Efes, on 28 December 2012.

After a series of mediocre performances in the first round, he led Greece to a victory over the Russian National Basketball Team in the quarterfinals, and orchestrated a major comeback against the French National Basketball Team in the semifinal, when Greece was down 7 points with 47 seconds left on the clock.

In the final against the German National Basketball Team, led by the prodigious NBA All-Star Dirk Nowitzki, Papaloukas scored 22 points, leading Greece comfortably to its second European title, eighteen years after its first win at the EuroBasket 1987.

His most formidable personal recognition came on 26 January 2007, when he was voted by fans and journalists as the FIBA Europe Men's Player of the Year for 2006, topping the likes of Nowitzki, Gasol, and Tony Parker.