Interesting

[BatmAngelus]

These are all the remaining ones I can argue:

And of course, the guy with a bomb in his stomach just happens to be captured and in jail at the exact time the Joker needs him.

I'll have to watch again, but in reading the script, the guy with the bomb in his stomach is in jail at that time because he was one of the thugs in the truck with Joker.  No coincidence here.  It only proves that Joker did, in fact, plan to get caught.

After Gordon visit Dent, Maroni just happens to be in the hospital and just happens to have an attack of conscience and tells Gordon where to find the Joker?! It?s so pathetic and contrived I can?t even believe it!

Well, the Joker kidnapped Lau.  Since Lau was the only one who knew where the money was, we can assume that he confessed to Joker where it was and Joker then called up Maroni and the Chechen to where the hiding spot of the money was, planning to kill both of them.  Only the Chechen showed up.

Maroni probably figured that Joker wouldn?t be completely loyal to them and simply hand Lau and the money back.  Maroni basically wanted the city back for himself, but he knew the Joker probably wasn?t going to leave anything for him or even let him live.  Between Maroni and the Chechen, Maroni ended up being the smarter of the two in staying away from the Joker?s trap. 
He ?just happens? to be at the hospital because he probably found out that the police commissioner was visiting Harvey Dent in the hospital and went there to catch him.

The Ferry plan only came about at the last minute so it?s not like it was along-standing plan giving the joker plenty of time.

The ferry plan came about because it was the only available option.  The Joker threatened the bridges and tunnels and knew that the ferry was the only option left.  He probably wasn't going to do anything to the bridges and tunnels at all.  Just make them think he was.
Meanwhile, the cops were too busy searching there as Joker had his men load up the ferries with the explosion.  He basically tricked everyone into falling into his trap.
How the National Guard missed seeing the barrels of gasoline is another story.
Overall, I'd say that The Joker in this film didn?t react to people?s actions- he planned his crimes around his predictions of Gothamites' every move.

Lucius Fox says something along the lines of ?You took my sonar concept and applied it to every phone in the city?. Someone explain to me how this is possible! Given the sonar technology has to be embedded in the phone itself (as we saw when Fox was in Hong Kong and left his sonar phone at security), are we expected to believe that Batman has the technology manually implanted into *every cell-phone in the city? ? a city which, incidentally, has 30 million inhabitants, according to Fox.

Someone needs to address this, but I always thought until now that Batman had changed it so he could pick up all cell phone frequencies, rather than changing everybody?s cell phone into the one Lucius gave him.  The former is probable considering Bruce?s scientific intellect and the latter is improbable considering that he?d have to turn every cell phone into the one Lucius gave him.  For now, I'll go with the former.