Covalent bond deformation
There are two distinct phenomena, which are somewhat related. 


Dynamical effect of molecular vibration  


Bonds do vibrate like springs, and as you said they can store energy by changing its vibrational state. Like a string, the more energy stored in the vibrational motion, the larger the magnitude of such vibration.  Different from a spring, such vibrations are associated with discrete quantum numbers, and even at absolute zero temperature, such vibration still possess a zero-point energy and can never stop.


Non-dynamical effect that change the statistical average of bond length


Molecular vibration often (but not always) occurs at an extremely short time frame, and the vibration itself is often (again not always) of a very small magnitude, so when we refer to bond length we often mean the average bond length over time.
    Normally a molecule stays near the bond length where the energy is the lowest.  There can be a few reasons for a the average bond length to change while keeping the connectivity of the molecule intact, with some examples:


Each conformational isomers will have different bond lengths.  Usually this is a small number.  Examples of large bond length change between conformational isomers with the same bond connectivity are those with Jahn-Teller effect. 
By changing the vibrational state of the molecule, the average bond length can be different.  Usually, because of anharmonicity, the higher the vibrational state, the higher the average bond length.  Temperature change, pressure change, collision or photon excitation (especially infrared light) are the most common causes of a change in vibrational state.
Through inter-molecular interactions or external forces, the potential energy surface of the molecule can be changed so that the energy minimum happens at a different distance.  In this case, the bond length will change, but the energy stored in the bond will not change.  This can be achieved through external electronic field, or intermolecular forces such as electrostatic force from an ion, hydrogen bonds, charge transfer, electron donator/acceptor interaction, etc.