My question is simple (although the answer will most likely not be): I\'m trying to decide how to implement a server side upload handler in C# / ASP.NET.
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IHttpModule gives you much more control, you can basically control all of the traffic directed to your Web application. IHttpHandler gives you less control (the traffic is filtered before it reaches your handler), but if this is sufficient for your needs, then I see no reason to use the IHttpModule.
Anyway, it's probably best to have your custom logic in a separate class, and then just use this class from either IHttpModule or IHttpHandler. This way you don't really have to worry about choosing one or the other. In fact, you could create an extra class which implements both IHttpHandler and IHttpModule and then decide what to use by setting it in Web.config.