I am a fairly new adopter of jQuery, but a long time software developer. One of the things I really like about the jQuery approach is a mindset to keep implementations clean and maintainable. Having said that, it is easy enough to take the unobtrusive paradigm down the path towards unmaintainable systems without some good guidance.
Several things can happen (in no particular order): 1 - application developers can load up one or more js include files with a lot of seemingly unrelated javascript. Finding the source gets hard to do. 2 - the developed jQuery javascript hides the intent of the application. i.e. When looking at the markup, you can't really understand what's going on. 3 - the developed jQuery javascript is hard to follow. It seems as though spaghetti code never goes out of style 4 - developers throw some stuff in markup, other stuff in include files without a clear purpose thereby confusing even themselves two months down the line. Sometimes it was expedient, other times necessary, other times it was poor understanding of the app, and yes, laziness too. I've seen some older writing by Yehuda that point the way, but it sure would be great if there was a wiki or something that provided a thorough treatment. If something already exists, it would be great to shine a brighter light on it (I haven't found it yet). If not, are there folks willing to get something together; the entire community would benefit?