I think Sara and Greg worked very well together, you can see their real life friendship show through on screen. They seemed like they always had fun together. Also the "I came here for you Greg" scene in FannySmackin always tears me up.
I also love to see him work with Grissom because they play off each other so well and it's usually a funny moment. The ep 'Spellbound' is a perfect example.
But my fave character to see him paired with is Nick, because those two are great together, they have such chemistry and again the real life friendship comes into play. They can communicate with just a look and they usually have some funny moments because Greg always tries to impress Nick with stories about his past love life. From the very beginning (the pilot) those two shared scenes that were some of the funniest on CSI.
EXP:
Nick: "You beeped me from across the hall?"
Greg: "Yeah, I waved, you didn't look up."