Nolan North and Emily Rose did motion capture sequences for the game.
Any time Drake is wearing a wet suit the brand is clearly stated to be Otssel, which is a nod to Daxter of Naughty Dogs Jak and Daxter series. There's even a little stylized Daxter face on the sleeves. Additionally, the Naughty Dog Paw-Print Logo can be seen on the rear of the collar on Drake's wetsuit
The sticker on the jetski is also on the shirt of Ellie in The Last of Us, which is another game by Naughty Dogs Inc.
A Precursor Orb, a reference to Naughty Dog's Jak and Daxter series, can be found during the game's story by Nathan Drake, and is identified as a "Strange Relic". This Easter-Egg would remain a constant through the following sequels.
Nathan Drake was envisioned as more of an everyman character than Lara Croft, the protagonist of Tomb Raider; shown as clearly under stress in the game's many fire fights, with no special training and constantly living at the edge of his abilities. The director of the game, Amy Hennig felt a heavily armored, "tough as nails" protagonist with a large weapon was not a suitable hero, and decided a "tenacious and resourceful" character would portray more human qualities.