One notable difference I will add to Ganesh's answer:
System.Web.UI.HtmlControls and System.Web.UI.WebControls can be manipulated similarly at the server (many similar controls share many of the same properties), however only WebControls will have the most useful events at the server. (I say "most useful" because HtmlControls do have some events but they are typically not used very much, I've never used one yet.)
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Peter