Wow. I wish I’d run into this thread sooner…! 
Interesting questions. I pretty much agree with a majority of the above members’ answers to the interrogatives, but I’ll put in my two cent’s worth anyway…
1) Why the Breaking Bottle? - I always figured that bottle broke due to two reasons, these being: a) It adds a sense of emphasis to the current situation, and b) Remy was extremely angered at the time, sooo…voila’. Bad things happen when you get mad. Other than that, nubetre has me beat. 
2) Running Off Without a Motive? - Oh, there was a motive alright. For one thing, I’d probably be rather surprised myself if I was in that type of a situation. After spending months and months with this seemingly noodle-legged garbage boy, you’d think that you’d learn to know everything about him at some point. But, nooo! All of a sudden he pulls this rat out of his hat, literally…
Strictly speaking, however, I believe that the chefs just “refused to accept the fact that a rat could cook”, as has been quoted elsewhere (in a Ratatouille-licked book, if memory serves me correctly). T’was ludicrous enough already, what with Linguini’s unwarranted behavoir and all, but obviously a good majority of the chefs present couldn’t piece two and two together in that particular situation. I believe that Brad Bird (or either a Pixar employee or someone on this forum board) mentioned that Colette was truely the only other cook in the kitchen who really did believe in Gusteau’s motto, “Anyone can cook”, which is why she returned to assist Remy and Linguini in their seemingly foolish antics.
In a nutshell, the idea of a rat concocting gourmet delicacies was, perhaps, too much for some of the kitchen personnel to take in/handle.
3) Skinner in ze Ropes - Yeah, this was added purely for laughs and to keep Skinner out of the way so that the audience wouldn’t be distracted by anything else while the main story (Remy’s story) continued. Plus, it was hilarious. I’ve witnessed maybe only one time (out of the twenty-six times I saw Ratatouille in theaters) in which the audience didn’t clap during that sequence.
4) What was that Slap for? - There was no way Colette would have behaved the way she did unless she didn’t think that Linguini was completely out of it. As others have said, Colette continued to express her feelings toward the hapless garbage boy even after the latter dude woke up from that very abrupt slap. I often wonder whether or not Linguini ever told her that he was asleep the whole time…
5) Round Two? - Although Gusteau’s restaurant was shut down due to a “rattie overflow”…and though it is ultimately the responsibility of the superior entity/entities of the facility to evict and manage the rodential “income”, it wasn’t really Colette and/or Linguini’s fault that a rat infestatioin took place in the cafe, causing it to close its doors completely. Well, actually, it was their fault, but that’s not the point…! 
Hmmm. You know what, there is a loophole here! I suppose that they – they being Remy, Colette, and Linguini – simply waited until the heat blew over before setting up a fairly inconspicuous, yet profitable, bistro in an area some ways away from Gusteau’s. Plus, Anton Ego certainly put in a good word about Remy’s fine cooking, so the optimistic review must have spread. People who read the review may have also assumed that it was Linguini, not Remy, who transported Ego back to his childhood that fateful night, so when he and Colette constructed some new “cooking quarters” people probably flocked to the place for a sample of whatever made Anton Ego’s taste buds quiver. The food at La Ratatouille eventually become a modern day Pancake House and…voila’!
6) Wet Book a’ la Carte? - This kinda ticked me off, as well. I just took it for granted and naturally assumed that Remy had sat on his butt for days in that sewer, though why he would do anything as stupid as that is beyond me. (I remember that I was thinkin’, “Oh, for the love of Pete, Remy. Have you resorted to this? Go up and get out of there, for crying out loud!”) Anyway, getting back onto the subject of the book, I really have no idea how the pages could have been that intact, although the thing did stay afloat for a good duration of the river raft ride down the sewer. I suppose it didn’t get extremely soaked, thank goodness. I do like the idea of it being waterproof, though, even though I’ve never heard of such a thing as far as those types of hard-bound covers are concerned. (snigger)
So yeah. Nice observation, guys! 
Oh…and, kageri, you’re one of the most hilarious persons on the planet, dude. 
– Mitch