The way I see it Batman Begins is year one, the dark knight is year two. The Gotham Knight tie ins and the virals are the space in between BB and TDK. The reason why I believe this is something the Joker said in the trailer. He talks about how a year ago the cops and lawyers wouldn't have touched the gangs of gotham (doesn't that sound corny?). That may just be a flippant, passing remark, or it may be a reference to when Batman appeared. Both Goyer and the Nolans claimed TLH and DV as major influences and both are year long installments.
Year one
The main thing about Nolan's Batman is that his training is very short. In the comics Wayne disappears for years, during which time he is training himself for his return. But due to the whole League of Shadows thing Wayne's training is much quicker. He spends most of his time stuck as a petty criminal and in jail for a period of time. So say a few months of this first year are based on his training, then a few weeks returning to Gotham and getting ready. Then he starts taking down Falcone.
Once Ra's gone its normal batman, dealing with normal criminals and the gangs.
Year two
Begins with the Joker and the alliance between Gordon-Dent-Batman. We know from leaked pics that Bats catches Crane and fights the gangs. The trio then deals with the chaos and darkness that the Joker brings to the city. The Joker is eventually brought down. And the mob bosses go on trial, Dent becomes 2Face and he starts his rampage on the mob. Beginning with Maroni and Rossi?
Year Three
TDK ends with the rise of 2face which marks the beginning of year three, like Dark Victory. This is where the third film can come in, if there is one, Batman and Gordon cleaning up after 2Face as he goes about finishing off the mob. Eventually 2Face tries to kill Batman either in this film or in TDK. I personally hope to have Catwoman in this film as well, either as a replacement for Rachel or a rival. Nolan says the Penguin is hard to do, but Catwoman done as the simple cat burglar that Bats tangles with.
By this stage we could have classic Batman. The Wayne Manor rebuilt to its former glory but with "some improvements to the foundation in the south east corner". In the trailer the temporary batcave, under Wayne's penthouse, shows some sophisticated elements, like the batsuit's cage rising out of the floor. This improvements are included in the original batcave back at Wayne Mayor. TDK may even show this.