I would probably vote 2004 for being the most innovative and important top 3 in the modern era. All three entries had a significant impact on what the contest would become.
Wild Dances literally created the "Made for Eurovision Genre" which future entries have tirelessly copied with bombastic bops and spectacular shows for years. Lane moje gave Zeljko the pathway to becoming a Eurovision legend. Shake It continued the success story of Greece and become one of the primary blueprints of ethnic pop songs.
My own personal favorite top 3 would be 2006 because all three songs are among my all-time favorites. It also perfectly fit with-in Björkman's "Top 3 Triangle", which is "The Ballad", "The Pop Song", and "The Phenomenon". The top 3 of 2006 also felt like the spiritual successor of 2004's top 3 in many ways.
2007, 2009, and 2010 are also very solid overall. Then there are top 3s like 2012, 2014 and 2017 which have very strong top 2s but the third placer is far behind...