There is a huge difference between the three.
Lasers are the generic heavy beam weapons of the three. The damage they do drops of with range, they have to get through any shields or armor on the target, and they can be equiped with turrets for point defense work, or spinal mounts to give even more damage.
Mesons have half the range of the same size laser, they only do 1 point of damage regardless of the size meson. Their big advantage is they ignore all armor and shields so you start doing internal damage on the first hit. This can be huge against big, well defended targets as it could take a long time to get through the defenses with lasers.
Microwaves are a little different, they do 3 points of damage against shields, ignore armor, have the same range as the mesons as well. When they get through the shields however they only damage sensors and fire control. Against targets without shields they are devestating as they will quickly leave a ship blind and with no fire control. Effectivly this puts a target out of action very quickly. On their own they don't kill ships, but they work really well in support of other weapon types. I have been known to use them with particle beams to fight targets with heavy defenses as the particle beams will often have shredded the shields letting the microwave beams knock out the fire control. Switch targets and repeat, when all of your targets stop shooting back, you can then go back and destroy what you want to.
Brian