- it can be a bit hard to read and understand jquery code. You can make things happen in 1 line, and you can chain actions. So someone that is reading your code might have problems with it. (I always have trouble understanding jquery plugins when I'm reading the sourcecode).

- I'm guessing here, that a lot of users might abuse the class selectors ($('.someclass')). I think that might be way slower than selecting by id $('#myid') or even better $(document.getElementById('hello')). Class selectors should be used when you're going to work with an item collection.

- It doesn't place nicely with mootools. And although you can use the jquery noconflict thingie, still, it might be hard if you're using some plugins or code you just don't want to modify (I've had this problem in modx, which uses mootools for the frontend quick edit module).

- you don't need to care about browser compatibility, as jquery takes care of that. So, when you use it, you might not notice that IE still sucks

- it's free, it goes against everything the RIAA has taught us!

- it's kind of a big library (50k ?) which you always need to include even if you need the most basic stuff. I'm not a mootools user, but I think they let you choose which parts of mootools you want to download, and then they create a single file for you with only the things you need.