I think a lot of trilogies suffer from having one bad apple ruin the bunch. Jurassic Park, The Mummy, Indiana Jones, The Godfather, Beverly Hills Cop... that list goes on.
On a whole, the BttF trilogy is a testament to great foresight and writing. Say what you want about the movies themselves, but to contain an entire universe centered on time traveling in a comedic film without breaking their own rules or leaving open any gaping plot holes is a feat. If the Nolan Batman movies withstand the test of time like BttF and Star Wars then I think they're easily capable of holding the title of "best trilogy ever". Toy Story is top 5 easily with LotR. One of my personal favorite trilogies, however... The Mighty Ducks