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I love Thomas, personally. I know it is terribly popular too, though. My brother's name is Thomas Neil, which I think works well as a combo. Of your combos I like Thomas Nicholas and Thomas Robert.
I also love the nickname Tom, but usually spell it as Thom.

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Other combos from your list:
Thomas August
William Thomas
Thomas Laurence
Thomas Charles (Charlie sounds too nickname-y by itself, IMO)