My choices:
My favorite one is Eumenes of Cardia. Chief imperial secretary under ALexander The Great who had only recently commanded the household cavalry in a single small engagement. Became Perdiccas' chief commander, killed the experienced general Craterus, beat up on the others in the area, was nearly destroyed, cunningly escaped from Nora to raise an army in the east where he defeated Antigonus twice. On the second time he defeated him, Antigonus managed to capture the baggage train, and through a deal with the Silver Shields, got them to betray Eumenes and hand him over. Overall, he nearly single handedly held the empire together, being completely loyal to the Argead line.
Other honorable mentions:
Dirk already mentioned Metellus Pius, I would add Marcus Claudius Marcellus, who was fairly successful in Sicily (captured Syracuse) and against Hannibal at Nola, before succumbing to one of his ambushes. Overshadowed, obviously, by Scipio Africanus. On the same note, Claudius Nero, who was successful in Spain before Africanus came and then by a stroke of tactical genius, defeated Hasdrubal at Metaurus, is also often forgotten due to Scipio.
There's Titus Labienus, who was a damn good commander, and I'd say nearly as good as Caesar. He was Caesar's chief legate during the Gallic Wars, and fought against him in the civil war, nearly defeating him at Munda.
Sextus Pompey: younger son of Pompey The Great, managed to wage a guerilal war in Spain after Munda, then took control of Sicily and dominated the seas, saving any proscribed senator and strangling Octavian in Rome by cutting off the grain supply. Crushed him on two separate occasions, nearly killed him, and on the third try, he barely lost. Never had the forces to invade Italy, but still very nearly brought down Octavian. He's often overlooked when people talk about the liberatores and the second triumvirate.