Well going through the 3d games there's Dodongo's Cavern, the Fire Temple, Dragon Roost Cavern, Goron Mines, the Earth Temple, and the Fire Sanctuary. Dodongo's Cavern is too easy to really be much fun. The Fire Temple isn't bad at all but it's definitely my least favorite adult link dungeon in OOT. I didn't like how it's relatively more linear than at least the Forest and Water Temples, having to fight the same miniboss twice was boring, and the dungeon item was pretty useless outside the dungeon which always bothered me because the hammer is so commonly used in A Link to the Past. Dragon Roost Cavern is a dungeon that I don't have anything negative to say about. I liked how it felt natural within its environment (with the outside parts of the dungeon reminding you where you are), and for a first dungeon it wasn't easy.
Goron Mines is a dungeon that often is praised based on my experience, but it was one of the least interesting and exciting dungeons of Twilight Princess for me. Having you use the iron boots as magnets was cool but became tedious for me really fast due to the slow movement. Like in other Twilight Princess dungeons the miniboss of the Goron Mines outshined the main boss which was one of the most forgettable ever for me. Also the idea of splitting up the boss key is genius, but effectively was wasted on a super linear dungeon design. There's no point to splitting the key up if you're just going to pick them up on the lone path through the dungeon.
The two fire dungeons of Skyward Sword were my two least favorite of the game. The Earth Temple was super short and rolling a ball isn't as much fun as it looks which is a shame since that's how half your time in the dungeon is spent. The Indiana Jones moment was really appreciated by me though. The Fire Sanctuary is better than the Earth Temple IMO but not by that much. There are just not a lot of interesting puzzles or enemies. It's just a lot of rooms and that's about all.
So in summary it's pretty obvious that I generally don't like fire dungeons. I don't dislike the theme at all; it's just a coincidence that almost every fire dungeon disappoints me. The only two ones that stick out as positives are the Fire Temple and Dragon Roost Cavern. I'd give the edge to the Dragon Roost Cavern because I don't have anything negative to say about it and it is a pretty well-designed dungeon.