<p>I've been using user controls extensively but never use a HttpHandler and was wondering if I am doing something suboptimal or wrong</p>

Unfortunately your question is a little like "Should I use a sandwich or a cement mixer".  HttpHandlers and User controls are completely different things.
HttpHandlers are used to process HTTP requests.  For example, if you wanted to dynamically create an RSS feed, you could write an HTTP handler that handles all requests for ".rss" files, creates the output and sends it back to the user.
User controls are used within ASPX pages to encapsulate units of functionality that you want to re-use accross many pages.
Chances are, if you're using user controls successfully, you don't want to use HttpHandlers!