I'm forwarding this to a soon-to-be ophthalmology resident fiend. To make his read more functional, please describe your symptoms more specifically.
These are just some questions I came up with. It's not a validated screening tool or anything like that:
When do your eyes hurt? Do you experience loss of vision? Blurry vision? Does it feel like you're in a tunnel? Do they hurt the same on the weekends? Holidays? Summer vs winter? Do you have seasonal allergies? What medications do you take for seasonal allergies? Are your eyes red and irritated? Do you have headaches? Do you feel nauseated? Do you feel physically exhausted, like you couldn't hold your arms up to comb your hair? Do you experiences auras? Have you recently lost weight? Gained weight?
The more people who could answer the questions, the more useful it might be, at least in painting a picture of what the common symptoms are.
This not medical advice. If you are seeking medical advice, you should consult a physician. That said, I'm interested. Having been all the way to an orthopedist and having a office ergonomics study done several years ago (my issue was numbness in my hands, fixed with proper positioning), I empathize.
Here's a search of the PubMed database to get started on further reading:
http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=D...
Honestly, my brief survey of the literature suggests that the usual culprits are at play and there's nothing particularly evil about computers:
1) Make sure your terminal and keyboard are situated so you have good posture (that whole sit-up-straight thing really works). Otherwise the strap muscles of your neck and head will definitely get strained throughout the day, leading to a headache.
2) Loose weight. Sleep apnea is a common cause of headache, which may be mistaken for eye pain. Type 2 diabetes is at least partially reversible with weight loss and is famous for causing numerous eye problems.
3) Take breaks. Your extraocular and intraocular muscles move your eyes constantly. 5 times per second. This means two things: "eye strain" probably isn't a muscular problem. 2) A lot of that movement helps monitor your environment and helps your brain construct better 3D representations. Staring at a flat screen of constant brightness may well screw with your brain. This is entirely speculative on my part, but I suspect it is similar to the headaches one gets in the fog on a ship at sea or in the desert: there's so little detail to train your eyes on. Alternatively, it may be similar to the experience of driving at night in the rain. The constant near-to-far ranging and trying to filter rain from road can definitely cause a headache.
4) Most reports are favorable toward anti-glare screens. I think this is at least partially missing the point that antiglare screens are also polarizers that cut down about half the emitted light. At the very least, the two effects are difficult to untangle. I suppose if you have a large window behind you, then the anti-glare value might be helpful. Otherwise, I'd say save your money, dim the screen, and use Flux. That said, one study looked at blink rate as a proxy for asthenopia and found anti-glare coating reduced blink rate. I'm not sure how far to follow that though because the activity was watching a DVD, not actively typing text.
5) Some studies look at age. Not much you can do with that one, my friend.
6) One study looked at environmental vibration. So, I suppose, if you're writing code in a plane or on an oil rig, you should use a larger font. Or find dry land.
7) Think about radiologists. They do pretty much all these things: good posture, dark room, no windows (no glare), they take breaks, and the old doctors (faculty) get new doctors (residents) to stare at the screen whenever possible :-)