So far what I've done, is go: Forest Temple, Water Temple, and I just started the Spirit Temple, but I won't be able to finish that cause I need the megaton hammer... who else has beat these temples out of order? Can you get Zora's sapphire before you get Goron's Ruby?
I do this all the time. You don't need the megaton hammer to finish the Spirit Temple (in the regular quest, master quest does require it), try it yourself and see. The door you would open with the megaton hammer just leads back to the first room of the dungeon and there isn't anything special in there anyway. And you can easily get the Zora's sapphire before the Goron's ruby by leaving dondongo's cavern once you get the bombs.
Here's something for you to try that I'm doing right now (no glitches required) upon becoming adult link in this order:
1. Get Epona
2. Get Gerudo Membership Card (tricky but possible without the hookshot)
3. Complete the Ice Cavern
4. Get the Hookshot
5. Get the Longshot (the first 4 keys in the Water Temple do not require the bow so you can complete up to the longshot without it)
6. Cross the River of Sand in the Haunted Wasteland then go through the Poe's path without the Lens of Truth. Get the Requiem of Spirit (before beating any Temples, kind of crazy yes)
7. Complete up to the bow in the Forest Temple
8. Finish the Water Temple
9. Finish the Forest Temple
10. Complete the Spirit Temple (note that you have to complete the Forest Temple to go back in time)
11. Complete the Fire Temple
12. Complete the Shadow Temple
13. Complete the Bottom of the Well
14. Finish the game
So in order of completion that's Ice Cavern, Water Temple, Forest Temple, Spirit Temple, Fire Temple, Shadow Temple, Bottom of the Well. I went back for the Bottom of the Well because I was doing a 100% run.
as long as you get the items from each dungeon you can do whichever ones you want but with some like the longshot and megaton hammer your so far in you may as well finish it. i remember my cousin couldn't figure out the forest temple so he did the fire temple and came back to it. im not sure if you can do the shadow temple before the water temple though, the event where bongo bongo escapes from the well might be triggered by compleating it. ill check it out on my next playthrough.
I've tested having every combination of Forest, Fire, and Water medallions and entering Kakariko (I think I did Fire and Water once but can't remember. I definitely did all the others though), and I've concluded that you must have all three to unlock that event. I think I did this on the N64 version so I think it's safe to assume the 3DS version is the same.
assuming you have to finish the dungeon once you enter, no grab item and go tricks,
Forest Temple can be 1st or 2nd
Fire temple can be 1st 2nd 3rd or 4th
Water Temple can be 2nd 3rd maybe 4th
Shadow Temple can be 4th or 5th
Spirit Temple can be 3rd 4th and 5th
Yep I agree, and the Water Temple can only be completed 4th without glitches by entering it for the Longshot and leaving since you need it to cross the river of sand (except in the N64/GC version you could backwalk across the river of sand but that's technically a glitch). The order would be Forest/Fire, Spirit, Water, Shadow but you'd enter Water before beating Spirit.