I am getting eyes pain and temple/forehead heacache playing Skyrim. (I also had similar problem playing Fallout 3)
What's strange is I don't get any problem playing other 3D games such as Deus Ex Human Revolution, Dragon Age 2, LA Noire, Shogun 2 Total War and so on.
I guess it has something to do with the 3D perspective projection or the how-smaller-a-further-away-object-is ratio or the color tendency or the camera distortion or the contrast or the brightness or... well, I actually don't know.

Do you guys have any idea on this?

I, too, have a bit of a problem regarding the perspective. It hasn't come to headaches yet but I've played games that did (Rift, Warhammer). I've noticed that in order to get a better view, I literally have to have my screen no more than 2 feet in front of my face. I have poor depth perception IRL anyway, so it makes it a little difficult for me to know how close my character actually is to something.

Distance viewing, to me, is a little awkward as well, but again moving my monitor closer to my eyes seems to help that. Sorry you're having headaches. You may also try adjusting the light in the room you're playing in. I had to turn off my overhead and turn on my desk lamp.

If your on PC change your field of view small FOV (which is in Skyrim) can create headaches cause your eyes are confused what FOV you should use is up to your own preference but your monitor size does play some role mine is 27' my FOV is set at 90 for most games. If your on Console then take a break look far out into the distance and back in at close and far objects.

How long do you play it for in one sitting on average?

Could be many things...

The HDR (Auto lighting adjustments), are waaaay over-done, and can "stress" your eyes natural adjustments to light. (It is redundant that it is even in the game. Everyone plays like they have cataracts, which is that eye-strain similarity you may be having.)

The "Screen-flashes", though they are mostly subtle, are still present. Most from HDR issues above, but also the "BLUR", which is similar to a flash, causing your eyes to attempt to "Focus", when they can not possibly focus on something. (Another useless effect of games that just causes eye-strain and undesired lag.)

Time... Disorientation... Due to the crazy fast days/nights, which can psychologically stress your mind. It is like virtual jet-lag for your mind. Your eyes, again, are constantly flip-flopping from over-bright days, and then trying to focus on details that you shouldn't see in the distance, at night... where the screen is just darker, not actually like night. You are focusing on distant objects that you wouldn't normally be focusing on.

Distance and angle... How far are you from the screen? Are you constantly looking downward at the screen, due to it being below your eye-line-horizon, or from you laying back on a chair/couch?

FOV (Field of view) distortion... Uncorrected FOV in the game, if you have made it wide, will cause eye-strain. Unless your screen wraps around into your peripheral vision, then you are stressing your brain, trying to reconstruct a normal image from a bent and twisted image. If it was in your peripheral vision, that would be correct, and no brain correction would be needed to undistort what you are seeing. (Another wasted effect that just causes issues.)

Do you wear glasses? Might be time for a new prescription, or time to clean them, or time to get a new pair if they are scratched... Your eyes keep trying to focus through the screen/eye reflections in your glasses... Play in darkness, with only a small light in front of you, not behind you. Lights behind you cast reflections on the surface of your glasses, reflecting your eyeball onto the mirror-like surface. Your eyes fight to look past that glare. Same with scratches or grime on glasses, or misaligned prescriptions.

Don't have glasses? Perhaps you need them...

Tis' the season for allergies... Cooped up in homes, with any form of ionizers or perfumed air-fresheners, or with dander-animals, will greatly cause nasal headaches... Just being arid, with the heat on, will do that to you too... Check your home air-filters... invest in hepa-filters for a month... unplug your Glade-plugins... unplug your ionizer toys that are pumping ozone into your lungs, numbing your sense of smell and causing ozone headaches...

Since you're not having problems with other games it's mainly due to the 65 degrees FOV, too bad it's tailored to play a few meters far from the TV. As others said if you're on PC you can change it to your needs [it's 90 for me]. Also, if you play on first person view you have to take into account the camera bobbing effect when you use melee weapons. A tiny camera bobbing effect is also there when you run in first person mode with your weapon sheathed.

In WoW, several years ago, the expansion that had the underwater area in it. In that area, I always had a problem feeling kind of sick to my stomach, visual issues.

So, one day I posted on the forum, and turned out there were quite a few other players with the same problem, including some that had gotten seizures playing there.

Blizzard must have read several threads about that, because they published a patch that changed something in that area that reduced the problem.

I haven't had a problem yet in Skyrim, and I play an average of 8 hours per day (with several breaks during game-play.)

So, games can affect players in different ways.

I get headaches. Someone at Beth said

'Herp! who has non-HD tv's anymore?'

'None?!'

'Yes herp cause lets make it a mess for non-widescreen/HD people'

I can't see my health bars, gold or weight. The screen is pixalated to oblivion and the text its really hard to read even with my glasses on it is like this to be fair which makes it rather annoying and hard to read especially when trying to have distance from the screen. Does not detract from it being a good game just... next time, sort it out. Three people I know have a similar thing.

The only real issue i have with Skyrim is motion sickness when using melee, so I don't touch melee with a barge pole. As for headaches, i only get them if I've played for a prolonged period of time in a badly lit room. If you don't already, try making the room brighter.

I too have experienced this, I thought it was just me, it hadn't occurred that it might be caused by the game itself... I have a HDTV about 5-6ft away from where I sit. Don't think Ive ever had this with any other game, hence why I thought it was just me.

Its likely the FOV is not set right for your situation. If you are on a console with a TV, try sitting closer or further away from the screen. If you are on a PC you can manually adjust the FOV. I am not sure why developers don't realize this and allow for easy changes to this in the games display menus.

Try playing less, or at the very least take breaks every 30 mins and get up and walk around for a couple minutes. Your brain might be getting confused by the conflicting inputs. Everything it sees says its moving around, but all the other inputs from your body say you are sitting still.

From having the same experience, I needed glasses. I was getting headaches, sore eyes and dizziness. Also, from experience of an associate, smoking w**d can cause problems playing games, dizziness even sort of black outs and fits.

- I am on PC and I did try the FOV 90 before, but it gives me another kind of uncomfortableness because the part of image radially far away from the center of screen is kind of distorted, and those part of image would moves too rapidly when I move.

- My monitor is placed at a distance of around 2.5 feet. It's just 20inch on 1600x900.... (wow, monitors are 27 inchs already now? i was kind of neglecting it) The center of the monitor is pretty level to my eyes, I don't know whether it should be higher or lower though.

- I totally agree those blurs are BRUTAL to the eyes

- I would get the problem very early so I think it is not about prolonged-skyrim-usage

- As for motion sickness I got that too, it is especially evident when I am running plus looking at the ground for ingredients and ore vein; or when I am moving inside crampy dungeon.

Try to play less than 20 hours per day too. I've heard that helps too

How long are you playing before you expirence these problems?

like, several minutes, it depends on the area though.

When in doubt, consult a physician. I was a very accomplished soldier with 10/20 vision, then, within a few weeks time I was getting symptoms like yours. Long to short of it, a blood test revealed thyroid problems. Meds haven't fully made it better. GET YOUR EYES CHECKED!!!!! A Blood test wouldn't hurt either!

My eye-doctor says to live by the 20-20-20 rule. Every 20 minutes you should look at something over 20 feet away for at least 20 seconds. It really helps.

My Dr. suggests the same.