The short version: 17-year-old Marcus Yallow and pals are cutting school one afternoon in San Francisco when terrorists blow up the bridge. When the kids attempt to get medical aid for their friend, they're instead arrested, interrogated, and treated like terrorists. Upon release, Marcus discovers Homeland Security is conducting massive searches, surveillance, etc., and decides to convince them it's not a good idea to treat US citizens this way.
Things escalate, somewhat.
It's a technical book, with much talk of Linux, RFIDs, crypto, public keys and so on, and definitely an American-toned book. It's also got a massive amount in common with Harry Potter and the Order of the Phoenix, even down to Dumbledore's Army and Delores Umbridge. The difference is, in Phoenix, there was a genuine threat (Voldemort) which the authorities denied, while Little Brother's authorities see everything unusual as a threat - where "unusual" is defined as "not like us or our simplistic software models." And they attempt to fix things with laws and badly-applied technology.
Just like they do in real-life.
And that's why Little Brother's important, of course. Phoenix is about protecting your loved ones in spite of the authorities; Little Brother's about protecting them from the authorities, as the authorities stomp all over your constitutional rights, which they've been doing openly on a massive scale since the PATRIOT act. Phoenix is an allegory, while Little Brother only takes a squint to see how close the US is to this, already.
 That's assuming you're a US citizen, of course. If you're not, then you're obviously a threat to the US, as you can tell whenever you attempt to enter it, with all the questioning, finger-printing, no-fly lists, etc.
 Frustratingly, this has much in common with a short-story I wrote in January but haven't yet finished editing. Damnit. On the other hand, Cory's story is much better.