For sure. It can be a place to distinguish yourself - show that you've done some research about the company itself, demonstrate some genuine enthusiasm - your resume will cover the facts, this is a time to show a little bit of personality (that's my view anyway!) - hundreds of people will be mailing jobs@____.com. It can be useful to make it all pretty and send it as an attachment too.
I ask because I work for a reasonably unique company and I have a heuristic that if the cover letter shows no idea of what we're about (i.e. somebody has read the website, understood our values) then I click reject pretty quickly!
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