Continuing musing on this topic, thought I'd draw up a list! These are not my absolute favourites over the years, but just the favourites year by year. At least where it meets a certain threshold of "favourite". And yes, it's clearly heavily leaning towards one particular writer, and not just when he was the showrunner.
2005 - The Empty Child / The Doctor Dances
2006 - The Girl in the Fireplace
2007 - Blink
2008 - Silence in the Library / The Forest of the Dead
2009 - The Waters of Mars
2010 - Vincent and the Doctor
2011 - The Girl Who Waited
2012 - The Snowmen
2013 - The Day of the Doctor
2014 - Listen
2015 - Face the Raven
2016 - (pass - sorry, can't say a favourite!)
2017 - Extremis
2018 - Rosa
2019 - (pass - sorry, can't say a favourite!)
2020 - Spyfall (parts 1 and 2)
2021 - Village of the Angels
2022 - Eve of the Daleks
2023 - The Giggle
2024 - 73 Yards
2005 - The Empty Child / The Doctor Dances
2006 - The Girl in the Fireplace
2007 - Blink
2008 - Silence in the Library / The Forest of the Dead
2009 - The Waters of Mars
2010 - Vincent and the Doctor
2011 - The Girl Who Waited
2012 - The Snowmen
2013 - The Day of the Doctor
2014 - Listen
2015 - Face the Raven
2016 - (pass - sorry, can't say a favourite!)
2017 - Extremis
2018 - Rosa
2019 - (pass - sorry, can't say a favourite!)
2020 - Spyfall (parts 1 and 2)
2021 - Village of the Angels
2022 - Eve of the Daleks
2023 - The Giggle
2024 - 73 Yards