It seems unlikely that Badboy or any of the enemies he rode on set him up, yet it's hard not to include them as suspects.  For information on these people check out the adversaries section.

It's possible that Tupac's death was a result of a record label war between Deathrow Records and Badboy Entertainment.  It's important to realize that both companies were allegedly funded by organized crime syndicates.  Deathrow, headed by Suge Knight, and Badboy headed by Puffy, had prior history.  At an Atlanta party in 1995 Suge and Puffy had words and their was an underlying tension of violence in the air.  After the party Suge and Puffy stood outside exchanging words when a rental car drove by with a 9mm Uzi; Suge was hit twice and his childhood best friend and bodyguard Jake Robles was killed.  Suge allegedly said to Puffy "You did this, you tried to kill me!".  Suge Knight bailed Tupac out shortly after and the war was on.

Although Badboy rappers traded disses back and forth with Tupac, anytime it came down to confrontation they were quick to turn.  In the intro of the Makaveli CD it says they "banned together to form a conspiracy to assassinate the character of not only Mr. Shakur, but of Deathrow records as well."

He after all, claimed Badboy was responsible for the setup and shooting he lived through in 1994.  He labeled Jacques Agnant an informant, and claimed he and King Tut, alleged Black Mafia members who helped fund BadBoy, set him up.  He blamed Notorious BIG and Puffy for the setup as well, since they were supposedly his friends and never warned him of the attack.  You can read up on the details of that situation here.  Whether or not they had anything to do with his being shot a second time around is unclear.  Mobb Deep who had a large feud with Tupac, mentioned the murder scene in one of their songs, with them as the shooters, but that seems like typical Mobb Deep story telling.  Jacques Agnant, who was involved in the situation and the possible setup of Tupac in the rape case, who Tupac labeled as an informant in the song Against all Odds, is suing Tupac's estate for $212 million dollars, and claims he can't find work and has had numerous attempts on his life.  He would have reason to want Tupac dead.  Also, King Tut was later killed.  It's possible Tupac had something to do with his death and maybe the result was retaliation.