In the penultimate episode of Buffy the Vampire Slayer, entitled "End of Days," Buffy meets a woman inside a small pyramid outside of the Sunnydale cemetery (this sounds bonkers; have to watch this episode again) who claims to be part of a secret female order that watches the Watchers. And then (spoilers)
she is killed by Caleb and never gets to explain anything more about the history of her organization.
So where did the Guardians come from?
The Guardians are the watchers of the Watchers, and date from the time of the first slayer. They only appear once, in the episode you mention (and haven't appeared in the later comic seasons yet either), and so no more information is available than what was in that episode. In particular, this is the conversation that the last Guardian has with Buffy:
GUARDIAN: We forged [the scythe] in secrecy and kept it hidden from the Shadow Men who -
BUFFY: Yeah, met those guys. Didn’t really care too much for ’em.
GUARDIAN: Ah, yes. Then you know. And they became the Watchers and the Watchers watched the Slayers ... but we were watching them.
BUFFY: Oh, so you’re like ... what are you?
GUARDIAN: Guardians. Women who want to help and protect you. We forged this centuries ago, halfway around the world.
We know that in ancient times there was a group of "Shadow Men", who created the Slayer. The Guardians were the 'Shadow Women' (i.e. the female mystics of that age and place), who clearly didn't trust the Shadow Men (or later, the Watchers). It's likely that they have assisted Slayers in subtle ways over the years, although the protection of the scythe was key to the Guardians who settled in (what became) Sunnydale.
The final part of their conversation sounds to me a lot like Joss Whedon acknowledging (apologising for?) the deus ex machina:
BUFFY: I don’t understand. How is it possible that we didn’t know any of this?
GUARDIAN: We hid, too. We had to until now. We’re the last surprise.
Some have theorised that Willow is or will be the first of a new line of Guardians. She (temporarily) physically resembles the Guardian when she uses the Scythe, and can sense the slayers:
WILLOW: I can feel them, Buffy. All over. Slayers are awakening everywhere.
DAWN: We’ll have to find them.
WILLOW: We will.
Between Season 7 and 8, Willow's magical power increases considerably; she does fit the "mystical magical female who knows all about the Slayers" profile (and has opposed those that are the new Watchers before). However, we haven't seen her doing much in the way of "guarding" so far, and in the crossover with Fray she's a lot darker than would be expected of a Guardian.
A mini-series is planned that centers on Willow (note that the page at that link contains significant Season 8 spoilers), so if this is the direction that her character is heading, we may see more hints of it soon. Perhaps this is the alternative path to "Dark Willow".
