CGI & motion-capture / Flash
Batman and Superman: Battle of the Super Sons
Final Fantasy: The Spirits Within
Justin and the Knights of Valour
The Little Prince (Council of Geeks) (partly stop-motion animated)
Mune: Guardian of the Moon (GKIDS)
The Peanuts Movie (Council of Geeks)
Puss in Boots: The Last Wish (Break Room of Geeks)
The Sea Beast
This had a limited theatrical run before debuting on Netflix, so I consider it a theatrical film rather than a web film.
The Secret Life of Pets (Council of Geeks)
Smallfoot
The Super Mario Bros. Movie (Break Room of Geeks)
Teenage Mutant Ninja Turtles: Mutant Mayhem (Break Room of Geeks)
The Wild Robot (Break Room of Geeks)
Flash animation
Aqua Teen Hunger Force Colon Movie Film for Theaters
Sita Sings the Blues (GKIDS) (also uses rotoscoping and other computer animation techniques)
CGI index
Flash index
action/adventure /
action comedy /
animated /
anime /
B-movies /
CGI /
classics /
comedy /
coming-of-age /
comix /
crime /
DC /
disaster /
documentaries /
drama /
dystopian /
family /
fantasy /
film noir /
giant monsters /
Halloween /
holiday /
law /
martial arts /
musicals /
mystery /
period /
romantic /
rom-com /
scary /
sci-fi /
Scooby-Doo /
serio-comedy /
short /
spies /
sports /
supernatural /
surf /
teen /
thrillers /
true story /
video games /
war /
weird /
westerns