Rather than rank them, I’ll just list some of the challenging aspects of each.
Blackrock Depths
Finding a group members that were looking to do the same parts of the dungeon as you: many people only wanted to run the prison section for the Ony quest chain, some just wanted to do incendius for the FR bracers, still others wanted emp runs. With the lack of AOE in vanilla, the lyceum was particularly painful (luckily I ran with a rogue who would stealth kill and loot the flame wardens). Remembering to put the loot to FFA during the lyceum was also tricky.
Lower Blackrock Spire
Finding a group for LBRS was often challenging because people didn’t generally like running it. Navigation was often tricky here, especially when attempting the shortcuts through the dungeon. In terms of fights, the troll area was probably the trickiest with the likely possibility for runners to bring adds.
Dire Maul North
Captain Kromkrush and the final area was probably the trickiest (fears would often lead to adds).
Dire Maul East
Mostly easy, except for the tree gauntlet towards the end - this would trip groups up pretty often.
Dire Maul West
Navigating was sometimes difficult. I feel like west was less popular than east and north so a lot of people weren’t that familiar with the boss fights - many of which would result in wipes if the mechanics were ignored. The last boss (the elf, not occulthar) also hit like a truck… and you were lucky if no one left the group after Occulthar thinking the dungeon was over.
Scholomance
Scholomance was very tough. The mob density in this dungeon meant adds during trash happened a lot, leading to wipes. The trash itself was also pretty intense. Again, many of the boss fights were doomed if you were unfamiliar with the mechanics - even the mini bosses before Gandling were no walk in the park.
Stratholme undead side
Strat UD also featured some pretty heavy mob density. Tanks had to be very careful not to overpull - and the patting gargoyles and invisible shades made the trash sections tough. The early boss fights weren’t bad, getting to them was tougher. The abomination gauntlet was a group killer as it was easy to accidentally trigger before the group was ready and was punishing for groups that weren’t using resources carefully or lacked the DPS to keep up with the waves. Rivendare was tough for groups that didn’t have a lot of lvl 50-60 gear.
Stratholme Scarlet Crusade wing
Live Strat had some tough trash pulls towards the beginning and it was easy to get overwhelmed with adds. The hardest part was probably the last few hallways with the battlemages that would wreck face if not properly CC’d.
I guess TLDR is that many of the instances were difficult because of navigation and trash more than boss fights. I always felt like it was an appropriate challenge and rewarded people who ran them often enough to be familiar with the layouts, patrols, shortcuts, and other minutiae that go unnoticed in today’s zergfest 5-mans.