Why skids?

Think about this: if you land a VTOL craft on an unpaved planetary surface, especially in mud or sand, the wheels will probably sink unless you have tires so large that stowing them becomes a problem. Given, then, that wheels are not required for liftoff or landing, there is some sense to using skids, since it spreads the weight out over a wider surface without needing bulky tires.
This thread should probably be in the main forum, since it's on topic.

That said, the biggest reason is simply that nobody likes putting wheels in their futuristic design -- they seem "retro", even if they make sense... so designers try to avoid them wherever possible, from Luke's floating landspeeder to skids on starfighters.
Maybe it makes more sense from an inventory standpoint? If you need to repair landing gear, you just need to frakenstein yourself a hunk of metal to put underneath the craft (that could maybe also be used as armor paneling or some such as well) rather than have a bunch of round wheels just sitting around to replace burned-up or cracked tires? Maybe metal lasts longer in space than some kind of semi-rubberish material would?

Also, is it assumed that these futuristic scenarios with the landing skids against the deck are frictionless and that it's either up to reverse thrust, artificial gravity, or automated landing systems to actually stop a craft? It always seemed like in the Wing Commander movie or BSG, there was some kind of friction there, but maybe my brain is falsely remembering sparks and just superimposing them in there? Sure hope so...a lot of these birds run on some kind of fuel don't they? Seems like a design flaw if there were sparks shooting off every time it accelerated or decelerated down the flight deck. :)
Well remember, you don't have to accelerate on the surface of the deck itself, or land on it either. In WC1, the fighters were launched from the tubes so the landing gear doesn't matter. In WC2, it appears that the do launch on the deck for a short period. In WC3 and WC4 (which I might remark, all the fighters have wheels on their gear) they take off and fly away. On landing, we see in all the installments of the game series that the fighter doesn't actually touch the deck until it reaches its parking area, such as the sequence in WC2. I always found it ironic that the fighters that were capable of wheeled landings and takeoffs never did it, and that the fighters with the skids never hovered.

From a practical standpoint, its also advantageous to have wheels on the fighters because then you are capable of towing them around the flight deck without having to power up the fighter so it can hover. It also prevents damage to the deck and reduces friction.
Some thoughts:

In modern cat launches, the aircraft is strapped in, and essentially thrown off the ship. (Okay, okay, it gets accelerated towards the end of the ship).

In WC2, that's simple enough to do - instead of strapping in the nosewheel, you either strap in all the skids, or simply put anti-grav in the skids and levitate them.

Similarly, if the fighter is out of power, you could strap it external anti-grav units to it with an external power source to levitate the fighter while you tow it away.
it could also be something like the mag lev trains (such as the bullet train in Japan), they are rather simple and wouldnt wear out since theres no direct contact.
Generally I believe skids are preferred for aesthetic reasons more than functional. For most sci-fi themes, including Wing Commander, the craft seem to be able to levitate, further eliminating the problem of friction.

As for a possible advantage, they would be easier to secure to the deck of a starship to keep them from rolling about on their wheels (modern carriers chain aircraft down to the deck to keep them from rolling around). As to the claims that skids could land where wheels couldn't I'd have to disagree as, on the grand majority of craft I've seen in sci-fi, the foot print of the skids are not that much larger than you could achieve with wheels.

Wheels are easier to work with when you have disabled craft to deal with though as you can simply drag them to maintenance, though the landing bay is usually the maintenance bay as well on most sci-fi carriers. Though even that could be overcome by killing the gravity generators on the flight deck, then it would just sort of float, weightlessly and you could conceivably move it by hand at that point, it'd just be tough for you to get its momentum going.

Planetside is where you may have difficulty. In a sci-fi universe I roleplay in, the fighter my character pilots has wheels for landing and movement on the ground since it lacks dedicated lifting thrusters, and the lateral thrusters lack the power to counter gravity.

Those are just a few considerations. Though I do believe aesthetics play out more than any consideration for functionality in most cases.
Ince Wing Commander has both types of landing gear, It seems that each gear style is used where they would be most appropriate to the type of craft. Skids have the added advantages during launch. They can be easily magnetized, and therefore fit better into magnetic levitation catipults then wheels. Wheels have advantages while landing. Thus, it suggestable that which system is better depends on the role the fighter will have: skids where launching is a priority for instance. This would explain WC2's launch sequence, where the fighter stay on the catipult (and therefore close to the ship) until they obtain the needed speed to take off.