1. Streamline your (x)HTML
Many jQuery based features I have come accross involve a lot of extra HTML tags used for the UI that is not irrelevant as far as the search engine spiders are concerned. There are two main ways to ensure your HTML is slimmed down:
a) Dynamically add elements after the page load.
Below is an example to add a callback form to the page after the page has loaded.
b) Optimise the structure to remove unnecessary code.
Even better than adding code dynamically its removing it all together if it is not needed, one of the main cause of excess code is divitis , so have a look through your code and see if you really need that wrapper div or with a bit of clever CSS can you target the content in a different way?
2. Avoid blank/useless links
A better method is to use some other element such as a span as the trigger then dynamically add an on click listener.
This may seem slightly contradiction of the previous points, however if any SEO relevant content is not available when your script is disabled then it is likely the search engine spiders cannot find it. For example if you are loading relevant content via AJAX then from an SEO point of view it is useful to have a link to a static version of this content on the page too.
4. Code your javacript to fit your HTML and not the other way round.
5. Keep your script to external files