If you have a half-decent host, chances are these aren't network timeouts but are rather due to insufficient hardware which causes your server-side scripts to take too long to answer. For example if you have an autocomplete field and the script goes through a database of 100,000 entries, this is a breeze for newer servers but older "budget" servers or overcrowded shared hosting servers might croak on it.
Depending on what your Ajax operations are, you may be able to break them down in shorter chunks. If you're doing database queries for example, use LIMIT and OFFSET and only return say, 5 entries at a time. When those 5 entries arrive on the client, make another Ajax call for 5 more, so from the user's point of view the entries will keep coming in and it will look fluid (instead of waiting 30s and possibly timing out before they see all entries at once). If you do this make sure you display a spiffy web 2.0 turning wheel to let the user know if they should be waiting some more or if it's done.