The most famous instance of crucifixion I can recall in Roman history, barring that of Jesus, is the crucifixion of the last of the slaves that had fought under Spartacus in the Third Servile War. After a series of battles in central and southern Italia (first against the consular legions, then against the six legions raised by Marcus Crassus), Spartacus and his slave army were finally cornered between three armies. First, the army of Gnaeus Pompey returning from his victory over Sertorius in Hispania. Second, the army of Marcus Lucullus, pro-consul of Macedonia, landing in Brundisium on the heel of the Italian boot. Lastly, by the dogged pursuit of the army of Marcus Crassus which had been bypassed in Bruttium. Crassus finally cornered the slave army and heavily defeated them and killed Spartacus at the Battle of the Siler River. Some 5,000 slaves escaped the battle, to be later killed by Pompey's legions approaching from the north. A further 6,000 slaves were captured by Crassus, and were made into a ghastly warning. The gladiatorial school that Spartacus and his fellows had escaped from to begin their rebellion was in Capua, a city famous for the quality of the gladiators it produced. Crassus crucified all 6,000 of the captured slaves along the road between Capua and Rome, some 200 kilometers. This means every 100 feet or so along this road, for 120 miles, you would have seen the decaying body of a crucified slave, hanging from a cross a couple feet above eye level. They were allowed to rot away on these crosses, not taken away and buried after they had expired. This was the Roman warning to any slaves who would hope to follow in the footsteps of Spartacus. Appian describes this crucifixion of the 6,000 slaves in his Civil War, but Plutarch does not mention it in his Life of Crassus.

Crucifixion was a punishment usually reserved for slaves, pirates, and enemies of the state (Valerius Maximus refers to it as servile supplicium, i.e. the slaves' punishment). It was perceived as the most gruesome and dishonorable way to die: Cicero calls it in the "most cruel and disgusting punishment" (In Verrem). Seneca's passage on it is probably the most eloquent:

Can anyone be found who would prefer wasting away in pain, dying limb by limb, or letting out his life drop by drop, rather than expiring once for all? Can any man be found willing to be fastened to the accursed tree, long sickly, already deformed, swelling with ugly tumours on chest and shoulders, and draw the breath of life amid long-drawn-out agony? I think he would have many excuses for dying even before mounting the cross! (ad Lucilium 101)

Tacitus mentions in the Annals that executions were held outside the Esquiline Gate and that there was an areas specifically reserved for the execution of slaves. Josephus also reports on Titus' mass crucifixions, ostensibly to deter further rebellion, in Wars of the Jews (Book V). Plutarch's Moralia is the main source for the notion of criminals carrying their own crosses.

Edit: I forgot to mention the story of Julius Caesar's crucifixion of the Cilician pirates, whom he famously capture after being taking captive. It is recounted in Plutarch's Lives.