I haven't finished the game yet, as I still have 2 dungeons to go. As of right now, my order in Lorule has been Skull Woods, Thieves' Hideout, Desert Palace, Turtle Rock, and Swamp Palace. In Hyrule, I decided to do Tower of Hera before House of Gales because, having seen the demos, I was excited to do it. My order in Lorule, for the most part, is random; however, I completed the Desert Palace after the Thieves' Hideout because of the newly obtained Sand Rod, I figured it might be useful in a desert. My final dungeon order is probably going to look like:
Eastern Palace
Tower of Hera
House of Gales
Hyrule Castle
Skull Woods
Thieves' Hideout
Desert Palace
Turtle Rock
Swamp Palace
Dark Palace
Ice Ruins
Lorule Castle
I'm doing the Ice Ruins last because those freaking Lynels...