*First I'll say that this is mostly preference and you should take all answers into consideration.

Regardless, a proper bag should be used. A proper bag has at least 1/4" padding on the outside and separation for all lenses. The outside should have rigid panels to prevent flexing and distribute force from bumps. It should have strong zippers to prevent separation during travel.

Lenses should be stored to prevent telescoping. The best way to prevent this is to store the lens face down and keep the weight of the lens to prevent telescoping.

Damage to the lens element is unlikely when you have a lens cap and a proper bag with at least 1/4" padding. In order to damage a lens through the cap, a blunt force must be applied only to the center and not the ring of the lens. This is unlikely in a bag and why most camera bags have rigid panels, distributing force.

Keeping lenses face down also allow easier access for swapping of lenses since you can swap rear caps without removing the lens from the bag. Lenses should not be stored with hoods attached for long periods of time or further travel. Blunt force could damage the hood threads.

Padding should be aligned to prevent any two lenses from bumping. The force of two lenses hitting is a lot greater if there is no padding. The lenses should also have designated spaces that fit them snugly.

Flashes should always be stored straight and not in an angled position. Blunt force in any manner in an angled flash can damage the locking mechanism along with electronics.

Filters should be kept in their original cases for storage and hoods can be stacked inside each other loosely.