Friction
A system will lose energy as work is done against friction because of two surfaces rubbing against each other.
This can be solved by lubricating the system with oil, or using something which can roll (and so won't experience friction), such as a ball bearing.
Air resistance or fluid resistance
A system will lose energy as work is done pushing air or a fluid out of the way.
This can be solved by taking the mechanical system out of the liquid or gas and placing it in a vacuum.
Resistive losses
In an electrical circuit: