The comic and Timberlake debuted the faux music video on Saturday Night Live and later reprised the characters for sequels featuring Lady GaGa, Susan Sarandon and Patricia Clarkson.
Discussing SNL with Playboy, Samberg said he knows that 'D**k in a Box' will likely overshadow all of his future work.
"I consider Justin a friend, but those ['D**k in a Box'] guys are inseparable," he joked. "The funny thing is, Justin and I have become inextricably linked because of those videos. We've come to terms with the fact that in every interview we ever do for the rest of our lives we're going to get asked about 'D**k in a Box'."
Samberg also revealed that his favourite SNL sketch came in a Total Recall spoof where both he and Scarlett Johansson played the disgusting character Kuato.
"Scarlett was my favourite because it was funny and gross. It wasn't so much a kiss as licking each other's tongues. It was a kiss the audience definitely didn't want to see happen," he recalled.
The actor recently announced that he will not be returning when Saturday Night Live kicks off its 38th season in September.
Samberg next lends his voice to Hotel Transylvania, opening on September 28 in the US and October 12 in the UK.
Watch a trailer for Hotel Transylvania below: