I've seen the entirety of Disney's animated oeuvre, but I still rank 'Lilo & Stitch' as my personal favorite. The art design, specifically the use of watercolors, is wonderful and the characters are really well-done; the relationship between Lilo and Nani is so meaningful and realistic...it's leaps and bounds above how animated films usually write kid characters.
Of the early years, I think 'Pinocchio' and 'Fantasia' were Disney's crowning achievement of animation, and easily their greatest accomplishments. Of their middle period, I guess maybe 'The Jungle Book' was the objective best, but I prefer 'Robin Hood'. Of the Disney Renaissance, 'The Hunchback of Notre Dame' was hands-down their magnum opus (that "Hellfire" sequence...jeez), though I have a soft spot for 'The Great Mouse Detective' and 'The Black Cauldron'. Of the post-Renaissance, 'Lilo & Stitch' obviously takes the cake, but I think most of the movies made around that time were vastly underrated ('Treasure Planet', 'The Emperor's New Groove', etc.). Of the modern era, 'Tangled' was by far the most solidly written and animated, maybe followed by 'Big Hero 6'.
As far as live-action films go, Disney hit a lot of pure gold from the '50s-'70s; I think 'Treasure Island' and 'Mary Poppins' are my favorites. Of the mid-period, most of the cult classics definitely make my list: 'The Black Hole', 'Midnight Madness', 'Flight of the Navigator', 'Return to Oz', 'The Rocketeer', etc. (weirdly enough, I never liked 'Tron'). The live-action films really took a dive in the '90s/'00s (funny how the quality of the animated films and live-action films seem to fluctuate against each other)...'Pirates of the Caribbean' and 'The Muppets' are really the only stand-outs over the last 20 years, though I'll fight to defend my opinion that 'John Carter' was terribly underrated, just really badly marketed.