I do a lot of things, it really depends on his mood and how he responds to me. Sometimes I cup them with my first and middle finger, rub my thumb over the top of them and rub that little spot just behind them with my remaining two fingers. He likes that.
Sometimes I gently squeeze or massage. Sometimes I lick them or massage them with my tongue. I am also fond of gently scratching the underside of the balls. Although stroking is nice, I mostly like to cup them in my hand and shift the testicles around in the scrotum very gently.
Sometimes tugging is okay as long as it is gentle and it has the added benefit of helping them last longer.
Also he likes when I put one or both of them in my mouth and gently suck on them.