(ahem) bad wolf
Here are my thoughts on THAT TV show.

CAUTION: This is all total speculation, but since I have been reading people who claim to have access to SPOILERS (none of it convincing-sounding) you might want to not read this.

ALSO: the more I think about this the less convinced I am by any of this!!

1) I don't think they're likely to mine Dr Who tradition for an arch-enemy or nemesis -- this would be too confusing, and give too much ground to the fanboy militia.

2) They are giving us pretty hefty hints here [caution: site uses eerie and distorted sound of (?i guess) children singing 'who's afraid of the big bad wolf'.

3) So the general drift if not the specifics should be deducible.

And, working backwards from the 'hidden' message on the bad wolf site:

-- "Rose - Are you there? Are you getting this? You've got the point, haven't you? Rose...?": suggests someone (the Dr? Mickey?) leaving messages for Rose to help her makes sense of things. But really only serves to draw our attention to:

--the preceding text which stresses fiction / reality: " a fictional television programme"; "made"; "made by the BBC"; "placed"; and obviously: "If you're concerned by the thought that the universe has been irrevocably altered by an enormous experiment in neuro-linguistic programming, then just tell yourself "The Bad Wolf is not real. The Bad Wolf is not real. The Bad Wolf is not real.""

-- which foregrounds the idea in both the TV-news and reality TV episodes of humans being kept in a media-saturated dreamworld, which blinds them to 'reality' outside it. (i.e. neuro-linguistic programming = tv basically. (and whatever other beams cover up 'reality'. (which means: the revelation of the daleks is presumably not the ultimate revelation; there is still another 'bad wolf' force, lurking behind the reality we have seen so far.

-- i.e. basically I think we are dealing with the oldest myth in the book: the myth of myth (e.g. from Republic to Matrix)

-- or from the 'Theories' page of the badwolf site: "Bad Wolves can also be the bringers of dangerous knowledge of how the world really is, rather than just how we perceive it." i.e. the knowledge that we are in the matrix blah blah blah.

-- Combine this with the question the Dr asks about whatever century it is when he first looks down on earth from satellite 5, i.e. why hasn't history turned out the way it's supposed too. 100 years later he blames himself, but we also have to wonder if whatever alteration he is correcting was an alteration made to get him to intervene...

-- i.e. like being followed / led by 'bad wolf' around the universe, after the end of the time war, in which the same question arises: is he deciding his movement, or deciding to move at random, or is he being controlled, led, pushed: is this only an apparent 'reality' in which a larger force hidden to my knowledge is the 'real' prime mover.

-- The classic version of this is to replace 'myth' with 'reality', i.e. substitute the deeper reality for the merely apparent one. This is the standard 'radical' aesthetic-political tendency, in its spiritual (culture) and materialist (history) forms. The only interesting stories are the ones which play with this rather than repeat it. So for example in Republic, we know that the myth of the cave is precisely that -- a myth. i.e. Plato suggests that the distinction between reality / myth is itself a myth, i.e. reveals that there is no more profound reality at the same time as covering over this revelation by suggesting that belief in a more profound reality is inevitable and necessary. (Sorry, this is a post-Strauss reading).

-- Since I prefer stories which disrupt rather than confirm the 'reality is a myth' / 'there is a deeper reality' story I would love for 'bad wolf' NOT to turn out to have any coherent solution, i.e. not to be some sinister force which has been guiding the tardis / dr / rose etc., however I don't think RTD is a subtle writer, so I suspect it will.

-- More specifically, I wonder if the comment about a 'bad wolf' scenario in the early episode, combined with a reference to 'laxity in the multiverse' suggests a parallel worlds way of resolving the question i.e. this is an imaginary world created by or named bad wolf. The traces of bad wolf throughout this universe i.e. its internal coherence suggest a control from outside; as if the Dr was himself in a kind of tv show (ha reality tv within reality tv. how clever. :-( ) (As are the daleks -- i.e. if bad wolf means something it must be beyond them since a) something saved them from the time war and b) they were trying to avoid the dr, it was their victim who brought him to the gamestation; although c) I suppose they might have brought the dr in for the first round on sat. 5, but I can't quite connect this up)

-- but this would also explain the fascination with the internet in and outside the show (i.e. since a single corporation OWNS / controls the internet, all information within it is property, subject to manipulation etc.): the internet as matrix is echoed by bad-wolf-world as matrix in which the dr's path is determined.

-- the only interesting question this would leave (and I hope it's not this tedious, since this all seems quite lame so far) would be whether there was one or more universes, but I don't know about how this question and the other time travel paradoxes are usually resolved in Who-world. i.e. if there was one universe (which gets re-written / plotted as bad-wolf-world at some point (before or after the time war?) and can be turned back to 'normal' in the last episode (i.e. c.f. Rose's dad episode)) I would be happier than if there are more ( i.e. pretty much the 'they woke up and it was all a dream' version).

-- so if the bad wolf is not real, does that mean we ARE in a 'fake' world (tv); OR that we need to stop ourselves imagining that scenario, that there is another world, i.e we are in the only world, there it is real.