I don't know the keys in all cases...but something to get you started at least... (not including flagging either, unless the key results in flag, and I also know that I'll be missing some)
The Hole (not truely required, if you can still squish through the rock) - Classic
Paineel Proper (A Bone Key) - Only to open the elevator to get down into the city
Befallen - Several Keys needed throughout the zone to progress (removed?)
Najena - Several keyed areas within the zone
Sebilis - Trakanon Idol - RoK
Charasis (Howling Stones) - RoK
Veeshan's Peak - RoK
Sleeper's Tomb (Kerafyrm's Lair) - SoV
Skyshrine (formerlly, removed the key) - SoV
Tower of Frozen Shadow (1st level open, need keys to progress) - SoV
Acrylia Caverns (key removed) - SoL
Vex Thal - SoL
Torden, Bastion of Thunder (Key Flags you for entrance, also Towers are keyed (1 per group) as is the Agnarr event (1 per raid)) - PoP
Plane of Time (For true access, 85'ed in and looting a Time Phased Quintessence in phase3 will also flag you) - PoP
Beyond PoP, I don't know :(.