It's easily Butterfly Effect by Ray:
To be honest, if I was to compile my top ten, it would be entirely Ray and dots but that's boring.
I'll exclude Perfume and also Bish because if you know BiS you probably know Bish...
Yume by Maison Book Girl might be up there though, it's just majestic:
Bonus for having such an insanely creative MV (it features actual images pulled from people's brains using a special machine at some Japanese university). Okaeri Sayonara is up there as well, and is also thematically related to this video (whereas this video explores the idea of using the machine to see into someone's dreams, that video takes the idea and applies to someone on their deathbed)
Other favourites:
Which is probably an odd choice by them, but it has such a unique, ethereal atmosphere