At the moment, I probably have to go with this:
1. Veldora, Tensura
2. Paarthurnax, Skyrim
3. Ugin, MTG
4. Smaug, The Hobbit
5. Iskierka, His Majesty's Dragon
Some notable runners-up, just at the top of my head:
Draco, Dragonheart
Temeraire, His Majesty's Dragon
Lun'Kat, Beneath the...