It's true, as Matt says, that the root of the netroots is the defense of Bill Clinton, though I think that simplifies it a bit. To me, it all comes from a fundamental critique of the beltway media - politics-as-high-school, High Broderism, opinion that ranges from The New Republic to the Free Republic, the mainstreaming of horseshit from the right wing press, liberals-who-hate-liberals, and of course the Getting It Wrong About Everything.
Move On began by, you know, agreeing with Joe Lieberman, at least until Joe Lieberman decided that censure wasn't just a ploy to get impeachment off the table but his personal moral quest to punish that wicked wicked man for his wicked wicked blowjobs. Even The Nation, no Clinton fans, eventually woke up and realized that Ken Starr and his media sycophants were more troublesome than he was.
As awful as our media can be now, as awful as it was post-9/11, as awful as it was in the runup to the Iraq war, 1998-2001 is really the period when they collectively lost their minds, from The Blowjob through the Gore campaign, the contested election, and the post-Clinton "pardongate"/"white house trashing"/etc. Fox News, while annoying, was irrelevant because they really weren't any different than the rest of the media, where Lanny Davis represented "The Left."
The media problem was a political problem as well because for some reason the Democrats have a history of caring what these blubbering idiots think of them. So, "our side" takes it cues from Meet the Press and the Washington Post, constantly trying to please them and compounding the problem. But, fundamentally it's a media problem.
So, what to read? In no way am I trying to come up with a comprehensive list, and certainly one could reach farther back in time. None of this stuff "begins" at a specific point in time, really. If not for the return of the Iran Contra crew I'd probably not even start until we get to Clinton, but it's probably necessary to reach back for a bit of a reminder.
So, in rough order. First, the Reagan years. Haynes Johnson's book suffers from being boring, but it's a pretty good Reagan era primer, or at least I thought so a few years ago when I read it. Some of the general social critique I imagine is a bit dated.
Hertsgaard's On Bended Knee (Tom Tomorrow just reminded me to include this).
Next, Lawrence Walsh's book about Iran Contra.
Next, Eric Alterman's history of the punditocracy.
Then, Sidney Blumenthal's book The Clinton Wars, which I think is especially useful for its earlier chapters.
Gene Lyons' Fools for Scandal.
Conason & Lyons Hunting of the President.
For the fictionalized version, Philip Roth's The Human Stain.
David Brock's Blinded by the Right.
The book that Josh Marshall never wrote about "Clinton hatred" in the 1990s.
Marvin Kalb's One Scandalous Story.
The book that Bob Somerby never published about the Gore campaign coverage, or just go read the Daily Howler archives.
Toobin's Too Close to Call.
Late edition - Johnson's The Big Chill.
Alterman's What Liberal Media.
David Brock's The Republican Noise Machine.
Wolcott's Attack Poodles.
I haven't read any of the books about the press and the Iraq war coverage (aside from Boehlert's, which gives it some coverage), though I guess as a first stab I'd recommend Massing's articles in the NYRB.
The Unseen War.
Now They Tell Us.
Unfit to Print.
Iraq, the Press, and the Election.
Obviously the point isn't that I agree with every idea or opinion expressed in these books, but they provide a rough narrative strand which certainly informs my view of recent history and the media and one which I think is, to a great degree, shared in the "netroots."