It depends on the web site. If they have a link somewhere that says "click to download", then you're good (as long as the format is something Kindle-compatible). Otherwise, you are going to have to download web pages individually (via the browser), and use a tool like Calibre to convert it to Kindle format. If there are graphics, etc., it could be a real pain to create everything the way it needs to be to convert to .mobi format.
Edited to add: yes, check out the Calibre recipes. That could help tremendously.
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