Only one wants nr 1 (Atma ;D) so I will finish the game with all the crystals first.
I'm getting somewhere with my route now, hurray. Will post it later today.
EDIT: Just found a neat glitch that allows you to skip the Fire Rod in the Parallel Tower:
http://dehacked.2y.net/microstorage.php/info/3568/FireRodSKip.smv
Quite neat:).
EDIT again: Bah, you need the fire rod anyway. So it doesn't worked, too bad, it was nice:D.
Here's my route that I will use unless someone else says different:
Dark World:
Impa's Ways
Ether Medallion
Darunia's Cave, Cane of Somaria, Heart container
Finish Impa's Ways.
S&Q
Kakariko Village: Take the bow + a heart container
Buy super bomb
Nabooru's Hole.
If S&Q is faster than walking, then use it.
Saria's Gardens, Fire Rod
If S&Q is faster than walking, then use it.
Heart container in ?'s house
Get key in beach cave.
Get key at the Lake.
Upgrade sword and magic.
Rauru's dungeon
Either S&Q, or take the cave to get to the church, not sure about which is fastest.
Key in church + bottle (If needed, not sure yet...)
Ruto's Fortress
S&Q
Shiek's Hideout, Magic Cape
Parallel Tower, mirror
Light world:
S&Q to house, go to the forest and get the key
S&Q to house again, take the key in the rebel hideout
S&Q to house, go and take the key at pyramid falls + arrow upgrades.
Either walk from there to the tower, or else S&Q.