I have already killed everyone in one Dunmer Stronghold, and it just happened to be the one that had the master trainer for Enchantment I was going to go into another but i didnt want to find out i was killing someone else of value or importance, or if once i move the story line ahead they would stop attacking me. Any insight would be greatly appreciated.

I am sure that there are no storyline essential NPCs in the strongholds. There are one or two that are controlled by House Dagoth and one to the far north that is ruled over by a legion of orcs.

Hmmm that being said, I cannot remember if that one Dagoth you have to confront is in a stronghold or not...but, you have to kill him anyway.

• Andasreth: In the lower western section, there's a room with four Redoran guard corpses. Their banner shields are required items for one of Lloros Sarano's quests. Talk with him about Andasreth and he'll take them from you. He will not offer you any more quests after this, regardless of whether or not you've completed any of his other assignments. With this noted, you can learn the dialog topic "Andasreth" by asking Drulene Falen or Raesa Pullia how to get to Gnaar Mok, provided you have accepted or completed the main quest mission to Illunibi. On the upper level, there are a couple of hostile thief trainers. However, they can't teach you anything more than you can learn in town, and aren't really worth the trouble.
• Berandas: The bulk of the stronghold is safe, but underground, it's the staging area for an Imperial Cult quest. It's best to keep your hands off the place, but if you really want an artifact, there's a pair of unique boots laying around. Don't sell or donate them to the museum, or the oracle's questline will be impossible to complete. You should know by now that it's generally a bad idea to relieve artifacts onto NPC merchants.
• Falasmaryon: The victim of a Sixth House invasion. The Marksman master trainer is here, and has fled to a hut outside of the lower level (on the stronghold itself). He is friendly, and has used his skills to keep the cultists pinned down within the stronghold. If you want to save yourself some trouble later on as a Redoran, go to the Lower Level and kill Dagoth Tanis. If you want, you can get a chance to score some faction reputation and a unique ring later on if you get the ancestor ring off Irer Nervion's corpse on the lower level, but this is not strictly necessary. If you decide to go through with it, the ring must be kept until the quest to destroy Dagoth Tanis I talked about earlier.
• Falensarano: Here's an interesting one. What seems to have happened was a vengeful witch and Alfhedil Elf-Hewer -- the Axe master trainer -- moved in and chased the incumbent witch coven down into the lower levels of the stronghold. Both are coaligned with the player, but the previous coven is not, and has left behind a few summoned Daedra that Elf-Hewer and the friendly witch are oblivious to. No real quest association here, but the lower level packs a nice punch for the unsuspecting adventurer.
• Hlormaren: The hedge mage on the roof has a hit out on her. If you're thinking about joining the Morag Tong, and want her to be marked as a legitimate kill later on, leave her alone for now. There's another hostile, and also ultimately non-worthwhile thief trainer here, on the bottom level. No quests inside, so it's safe to give the complex itself a once-over. Do mind the slaves.
• Indoranyon: You already found out what the deal is here. The end boss is actually the enchant master trainer.
• Kogoruhn: Another stronghold under Sixth House control. Outside, on the corpse of an Ordinator, you'll find an artifact that must be turned in for a Temple quest. The most you can do with it is hold onto it until you stumble across the quest, since you can't return it early. The interior of the stronghold is the staging area for a part of the main quest. The Dagoth Goblet in the Dome of Pollock's Eye and the Shadow Shield in Bleeding Heart are items for this quest. Don't even try to hand them in early. The latter area is more easily accessible through the stronghold's back entrance inside the Ghostfence. The head of this place is the ash vampire Dagoth Uthol. If you're strong enough, kill him at your leisure, but try to sneak around and suprise him by initiating dialog if you can. Killing him now will help you out at the end of the main quest.
• Marandus: The stronghold has come under Redoran control. The NPCs outside are non-hostile. The NPCs inside, however, won't tolerate your intrusion, and will attack you on sight unless you have a ridiculous amount of Personality, excellent faction reaction toward House Redoran (IE, you aren't running around calling yourself the Nerevarine), and/or have truly magnificent reputation within House Redoran. They have no services, and no interesting dialog.
• Rotheran: The NPCs on the roof are interlopers. They are coaligned with the player, and you don't need to kill them. The Arena is the staging area for another Imperial Cult quest, and contains its associated artifact (the Ice Blade of the Monarch, which isn't strictly necessary to complete the assignmont in question, but will give you a reputation boost if you present it to the oracle when you collect the reward). The stronghold is safe as long as you don't talk to or kill the Dunmer slave. Otherwise, the oracle's quests are all hopelessly broken. Freeing the other (Argonian and Khajit) slaves here is gererally a good idea as it's a quick way to get invited into the Twin Lamps. Then again, you could always test spells on them.
• Telasero: The third stronghold that the Sixth House has commandeered. If you don't have the quest "Sondaale of Shimmerenne" for the Fighters' Guild active, everyone and everything there is completely expendable. Otherwise, in the southeastern room of the lower level, there's a damsel in distress that must be saved.
• Valenvaryon: An open-air shrine to Malacath has been constructed here, at the ekpense of the original stronghold's interior. Abelle Chiriditte -- the Alchemy master trainer -- got the right idea and took this opportunity to start selling potions out of the Propylon Chamber. Not wanting to turn down a potential customer, she's non-hostile. Everyone on the surface (barring Yadba gro-Khash, a pacifist) uses the elevated position of the stronghold to their advantage and will attack you as soon as they get a glimpse of you. Nobody will blame you for returning the favor. Everyone inside can be killed at your discretion, including two more hostile thief trainers.

Excellent. Thanks for that summary MB. It made for very interesting reading.