Desert: Sandship Skyward Sword: My favorite dungeon of the series, the Sandship wasn't exactly a desert themed dungeon but it was in a desert themed area so it counts
! Yeah I really liked this dungeon especially the shootout with the Bokoblins!
Earth: Earth Temple Skyward Sword: This is sort of a fire temple but I'm going down the list of themed dungeons on Zelda Wiki, so this is under Earth Dungeons so... Yeah I really enjoyed this dungeon and really liked the rolling ball parts, echoes back to Super Mario Galaxy but thankfully easier.
Electric: Lanayru Mining Facility Skyward Sword: I don't really care for this Dungeon but you know it's alright, better then the other ones unless you want to count Sandship again.
Fire: Fire Sanctuary Skyward Sword: In case it isn't obvious I really like the Dungeons in Skyward Sword, and Fire Sanctuary has got to be my second favorite of the game I thought it was just a very well made dungeon, and while nothing really stands out to me as being epically amazing but it did everything very well in my opinion.
Forest: Forest Temple Ocarina of Time: It was difficult choice between this and Skyview Temple, but I had to go with this one, it was just a better made dungeon, the mini-boss battle throughout the dungeon was a clever addition to the dungeon.
Ice: Snow Peak Ruins Twilight Princess: I HATE ICE DUNGEONS!!! The only reason I pick Snow Peak Ruins is because Ice Cavern was too small, and Snowhead Temple is my least favorite in the series second only to City in the Sky.
Light: Tower of the Gods Wind Waker: If this counts as a Light Dungeon I pick this, if not Ancient Cistern. I just really enjoyed Gohdan.
Shadow: Shadow Temple: Pretty good dungeon like the usage of the lens of truth, Bongo Bongo's pretty easy except when you run out of arrows...
Water: Water Temple Ocarina of Time: I love this dungeon, I really like how it was designed and didn't find it that difficult, was sorta annoying putting Iron Boots on, and Morpha was boring but other than that it was a sweet dungeon.
Wind: Wind Temple Wind Waker: I'd love to see more Wind Temples in future, but unfortunately the few that are in the series I absolutely hate the ones that exist, except this one which isn't terrible, but is boring, so... yeah.
Woof! That took forever.