I am in the process of converting an internal application to use more Ajax via jQuery. I am moving away from the standard code behind of the current ASP.NET application and incorporating JavaScript methods that are going to run client side. My concern is what is the best method for allowing this application to stay maintainable for those who come behind me.
Also, if you can, try to make a bit of an object-oriented design if you can. I was once on a project that involved a lot of jQuery/Javascript, and it did not have an object-oriented design, which made it difficult for us to develop and maintain it for a while. Over time, we actually ended up rewriting parts of it to make it better.
So my best advice is to think ahead, comment (like others have said), and make sure that you code your Javascript the same way you'd code anything else (as in, follow all the good design principles that you'd use on a server-side language.)