I am going through a pass for the second time. On the map it says it is cleared already. However, I am finding many creatures, Falmers and loot.
I thought if a place was cleared it didn't regenerate loot the way Oblivion did.
So, what does "Cleared" really mean?

Currently
Lootable
Eventhough
All
Random
Enemies
Deadbefore

Hell, I don't know

Thanks for the clever and amusing reply. I couldn't have said it better, and, of course, I didn't.

it means you have gone through it once and killed everything

It only means that you cleared it the first time around. It doesn't change back once it respawns, although that would be nice.

Once you cleared it the first time it does respawns back after some time past.

"Cleared" does not mean it doesn't respawn; it's just a tag to remind you that you already visited that place. A rather useful tag, if I may say so.

Has anyone worked out the in-game respawn time? Seems to be similar the 72 game hours of Oblivion, but some have suggested it's five game days?

On the 360 ( for me at least ), ever since the last patch, NO Cleared areas have respawn enemies. They have only respawn chests and loot.

I don't think (Cleared) Dungeons generate a new loot list from the leveled Variables. Granted, I haven't re-visited a lot of dungeons, but all I have that are tagged as Cleared, had similar leveled rewards as the first time, despite being upwards of thirty levels higher.

I think the same is true for the monster lists. The first Falmer dungeon I entered (Shimmermist by Whiterun) still has, at worst a couple of Skulkers and the one Shadowmaster Boss, while any other Falmer dungeons have a ton of Shadowmasters and Chaurus Reapers, which is actually kind of nice, as they're really the only thing that is a threat after level 50, since unless you're playing a Bosmer and/or using Poison Immunity, they can still take you out pretty fast if they swarm you.

there is a mod to set the number of days for respawning

It just means that you've been through there before.

They should have given it a "Visited" tag then instead of a "Cleared" tag. "Cleared" to me implies the place is clear since it's been cleared.

It isn't unrealistic that it does respawn. Also you have cleared it. At least once anyway. I just wish every dungeon did this. Because it gets a little confusing once every location has been discovered to work out which ones have been explored and which haven't.

I am on the 360 as well and areas above dungeons do not respawn after I go there and kill some things and on others they only partially respawn. This is on cleared and dungeons that have yet to be cleared, but it should be noted on the cleared dungeons there is no enemies whatsoever above ground. I think I began having respawn issue with either patch 1.2 or 1.3 I am also having problems with alchemy respawning as well.

Cleared indicate you have reach the target in the dungeon, killed an boss, read an dragon wall, might also be other indicators like picking up an quest object.
Now normaly it takes 30 days for respawn, however the game might override this if it need the dungeon for an quest. Some forts will also be occupied by stormcloaks or imperials then cleared.

Honestly its just a bugged statement. Ive gone into a Dwemer ruin before (the Peryite one I think) and I "cleared" the ruin even though I hadnt gone through 2 or 3 sub-areas.

I originally felt cleared simply meant you have entered and finished every area and every secret passage.

I've heard the respawn time for enemies in some dungeons is 30 days in-game time. But I have no proof of this it's just what I've heard... so don't hold me to it

Is it a common bug that enemies do not respawn above their respective dungeon?

This.

I don't really need it though because I can usually remember, but I can see why some would find it useful.

And it IS cleared - at least it was at one point.

Usually "cleared" means you killed everything in it, but today I got a "cleared" flag with enemies still in it.

No it doesn't even need to be actually cleared. All "Cleared" means is that you visited the place and met some specific goals, like defeat a boss or whatever.

It makes no sense whats however that a dungeon that was cleared (more or less) will remain indicated as "Cleared" after it isn't clear anymore. It really should just say "Visited".

I don't remember what patch I actually started having issues either. It seems like it was after this last one. It may have been the one prior, hell I can't remember. I have slept since then.

There are a few, and I mean few, that respawn any enemy what so ever.

Not every enemy, just the boss or dungeon objective like an dragon wall.