You can reduce the risk of micro scratches from rubbing microfibre cloths on lenses by washing the lenses under running water first to get rid of easily removable dirt.
Try to clean the lenses sparingly. Avoid perching glasses on heads if you still have hair. Oils are a downright nuisance on the lenses, unless you have custom cut Dillon lenses.
Don't rub too hard when cleaning old iridium coated lenses (e.g. Romeo 1) because the iridium can "flake" off!!
To avoid spider cracks in Romeo 1 lenses, wear the sunglasses like you are putting on a hat. You will look like a dork, but you'll wish you were laughed at when you look cool putting them on, only to find a spider crack in the upper field of vision.
Don't use the outside of the microfibre bags to clean your lenses if you routinely use the bag outside of a case. It tends to pick up environmental dust and particles and has the potential to scratch your lenses.
Avoid using the clear Oakley stands for some models of Oakleys. They can literally scratch both lenses on the inside due to the sharp pointy poorly designed edge of the stand.
If sending an O-matter frame to be custom painted, send the lenses as well, to be mounted, because incorrect mounting can cause frame chips in the worst place possible, the orbital rims (as requested by @SoulFulFrog).
If a custom cut lens is loose in the frame, use hot glue to secure it (@Chris515000), electrical tape (@SiRacer420).
When sending lenses to be custom cut to @Chris A Hardaway, make sure you send the frames to be fitted (if possible), because it is well known that x-metal frames especially vary slightly in sizes, even if they are the same model. Also the case with wires (@flyer aka "Wire King").