This is a grossly incomplete list. You can find a lot more films that used motion capture on Wikipedia or TV Tropes. Many of those mentioned I haven't seen, and many of the ones I have I wasn't aware of mo-cap being used, or I'm not sure how much it was mo-cap and how much it was normal CGI.

all CGI:
The Polar Express (2004)
Final Fantasy VII: Advent Children (2005)
Monster House (2006)
Beowulf (2007)
A Christmas Carol (2009)
The Adventures of Tintin (2011)
Mars Needs Moms (2011)

mostly live-action:
Star Wars (trilogy, 1999-2005; Jar Jar Binks)
The Lord of the Rings (trilogy, 2001-2003; Gollum)
I, Robot (2004; Sonny)
King Kong (2005; Kong)
Pirates of the Caribbean: Dead Man's Chest (2006; Davy Jones)
Avatar (2009; the Na'vi)
Paul (2011; Paul)
Ted (2012; Ted)
Paddington (2014; Paddington)
The BFG (2016; the giants)
Deadpool (2016; Colossus)
Beauty and the Beast (2017; Beast)
Alita: Battle Angel (2019; Alita)
Sonic the Hedgehog (2020; Sonic)