I'd have to say that these are two of my favorite endings for both song and sequence.
For Secret of my heart...what can I say, great song and one I was listening to way before I even knew it was used for Detective Conan. Kuraki Mai and Utada Hikaru were pretty much my introductions to J-pop artists. Anywho, the sequence for this ending very nice too. A nice little montage of all the events which led up to how things were at the time. The best part, though, is when Ran is singing along, and how Shinichi becomes Conan. To be honest, for that part alone made it for me. So, the song and the sequence goes very nicely together.
For Natsu no Maboroshi, another one I absolutely love, especially the song (and to date, I'd have to say that out of the Garnet Crow songs used for endings, this one is my favorite). I found the artwork very nice for the sequence. To me, Shinichi waking up, opening the door and facing himself was a nice set up. I also liked all the "Ran memories", so to speak from Shinichi's point of view and I like how it ends with that photo of those two when in the play. Just like with Secret of my heart, the music and the sequence complement each other very well.
It's a tough decision, but I'm going to have to go with Natsu no Maboroshi for this one.