Command points are needed to recruit new heroes. They are awarded after completing certain missions. You can also earn a Command point bonus by earning the fifth star mastery rank in each mission.
Energy
Energy is depleted in battles. It will recharge over time, or you can exchange energy with Facebook friends. Up to fifty units can be transfered per day.
Gold
Gold is awarded by leveling up or completing tasks. You can also earn a gold bonus by earning the fourth star mastery rank in each mission.
S.H.I.E.L.D. points
S.H.I.E.L.D. points are spent on research, buying items, and training. They will recharge. You can play on user-created maps to get them faster. Facebook friends can also transfer points to you.