This does contain spoilers, for Origins, Dragon Age 2, Witch Hunt, and Silent Grove....and just a smidge of Inquisition.
So, everyone has their theories about Flemeth. I just want to put my own thoughts out here. Agree, disagree, expand, theorize, flesh out my many gaping logic holes, whatever; do what you will. I'm interested in your responses.
(p.s. I am NOT going to site every single line of dialogue text I reference... you've played it, you'll remember it... maybe.)
RoraM. briefly mentioned that Flemeth may indeed be an Old God... that's where I'm going with this, by the way.
If Flemeth's an Old God, then I'm going out of the wimpy little limb and saying she's either Razikale, the Old God of Mystery (because who doesn't think Flemeth is mysterious?) or Lusacan, the Old God of Night (but, I'm leaning more toward Lusacan being the "Elder One" and the Vinatorri being some sort of Old God cultist. Again. Wimpiest Limb Ever.)
When the "Maker" (yes, I'm using quotation as his existence isn't proven) caged the Old God underground (not sure how that happened if the Maker doesn't exist, but this is all conjecture...as is almost all the lore in Thedas), she used a connection with the Fade to lure someone (probably an elven keeper or first) down to her cage to perform the ritual to place her within an object, or to perform or a ritual of possession. Perhaps she had convinced them to bring an ancient artifact (an eluvian), so that she could travel through the portal in her new uncaged body. She eventually came to possess a woman named Flemeth (and she ended up keeping the name), who was married to a noble man, who killed her lover. Flemeth then spent the years encouraging legend and myth about her to keep her true nature under wraps.
Now for a list of my supporting evidence (feel free to tell me if I got something wrong, it's been awhile since Origins.):
1. Flemeth using the connection to the Fade (does that make Old Gods demons?) to lure a victim to her cage in order to be freed...
This is possible, because in the lore of the origins of the Blight, the people of the Imperium, distraught at their banishment, sought out the Old Gods, who called to them through the Fade, taught them magic, and encouraged the first magisters to attempt to usurp the Golden City.
2. Flemeth's victim being a keeper or first... despite the trials of the Dalish, they still retained some of their knowledge and artifacts from the old ways. You can see this in Dragon Age 2 in your quest help Merrill, in Act 2, retrieve the Arulin'Holm, a tool needed to restore Merrill's Eluvian. You also see proof of eluvians continued existence in the Dalish Elf Origin of Dragon Age Origins, in which you and (Pol?) discover the strange portal (an Eluvian) in a cave.
3. Flemeth's long history of possession... In Origins, you discover, through dialogue with Morrigan, Flemeth, and even Leliana, that Flemeth has many myths surrounding her long and mysterious existence. Leliana or Morrigan (I can't remember specifically) tells a legend of a Flemeth, a woman married to a noble man, who, in a pique of jealousy, slaughters Flemeth's lover. This Flemeth could possibly be merely one more of her many possessions, and she decided to keep the name, either out of remembrance of a lover, or as a caution that love leads to betrayal. (Again! Say it with me! [kuh n-jek-cher]!)
4. In Witch Hunt, Morrigan speaks of Flemeth..."She is no blood mage, no abomination...she is not even truly human." I say this is pretty valid proof, because Morrigan knows more about Flemeth than we could ever even imagine.
5. There are rumors in the DA-verse, that even after the magisters razed the temples of the Old Gods and slaughtered their priests [because they felt betrayed by the Old God (as there was no Golden City for them to rule or they were unsuccessful when the Maker cast them out...which ever side of the lore you wish to believe), there were still obscure cults that worshiped the Old Gods. In Silent Grove, Yavana, one of Flemeth's "daughters" claims that the ritual of possession is a "gift". (Now, if that doesn't sound like sycophant, occultist worship...)
And Finally....
6. At the end of Witch Hunt, you track Morrigan down to a great chamber deep within the earth where she is preparing to escape... Let's see... Deep chamber within the earth (check! The Old Gods were caged underground), Eluvian, through which Morrigan has tracked based on knowledge left behind by Flemeth (check! I did theorize that she'd use one to escape!), and DUN-DUN-DUUUUN! - one giant freaking dragon skeleton! (which makes since if she simply leaves her previous body behind during a ritual of possession).
So, there it all is... there's so much more I could say on the subject, but it's pretty much theory on top of theory with no real proof ...and most of it makes me sound like Alistair (who I adore), pouting after being denied a feast of his dearest Fade dreams.
"But, but... cheese!"