Mine would have to be The Place Promised in Our Early Days because of its amazing animation,style, and music. I've probably watched it 7 or 8 times and it never gets old.
Honarable mentions - Cowboy Bebop Movie, Time of Eve(if you count it as a movie), Whisper of the Heart, and the Digimon Movie
My favorite is Akria. It was one of the first anime movies released in English and the artistry in it is amazing. The only problem with it is that the storyline kinda jumps in the movie, but it all makes sense if you read the manga series.
I really enjoy the Appleseed movies (Appleseed and Appleseed Ex Machina). Though I guess the art style really isn't anime, Ex Machina looked great for its time in HD.
I haven't seen very many strictly anime movies but I have always loved the DC Universe animated movies. Batman: Under the Red Hood and All Star Superman are the ones that stand out right now as being great, but all of them are very enjoyable.
I got lots of em that I really enjoy, maybe cause I'm a big anime fan. The ones that I thought were absolutely perfect were, most of the Studio Ghibli movies (Princess Monoke, Totoro, Spirited Away, Laputa etc.), Paprika, Appleseed and Apple Seed Ex Machina, Akira, Ghost in a Shell and Summer Wars.
Mentioned before but for me as well: The End Of Evangelion (OK can't recommend it without watching the entire series first). You either love it or hate it though, but it still gives me goosebumps and makes me smile.