If you go over to his house and notice something as subtle as a glass on the nightstand on your side of his bed that you never left there, it could be a sign someone else slept in his bed.
Or, maybe, the day after he told you he had ‘the guys’ over the night before, you discover every CD in his stereo from ‘guys night’ is chick music, like Adele, Florence and the Machine and Norah Jones. No straight dude invites the guys over and rocks that kind of music all night.
Perhaps, he's out of condoms and the last time you were over, he had a full pack. Sometimes, the smallest clues are the biggest indicators.