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In terms of IEEE style(IEEEtran) and ACM style(ACMsmall), respectively.

For example, when I mention Stack Overflow, should it be Stack Overflow [1] or Stack Overflow (www.stackoverflow.com)

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The IEEE reference guide includes websites among the references (see section R). I've also always seen websites listed in the reference section, and I've also cited them as such.

I'm not familiar with ACM journals, but the ACM citation style and reference formats webpage gives similar indications.

Therefore, cite e.g. Stack Overflow as

Stack Overflow [1]

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