I'm pretty partial to Edit+. It syntax highlights for just about anything. It'll allow you to change the colors. I've got a slightly older version and it'll let me change the background, but its not on a per-document basis like the syntax highlighting.
On a health note, do yourself a HUGE favor and get checked out by an eye doctor. I'd take a guess its not notepad that's killing your eyes but the fact you may be staring at the monitor for too long and/or a little too close or far away.
You'll want to take a break between coding runs and look at something off in the distance (and focus in on it). Do this for a minute or so before jumping back to coding.
Also, have you tried fiddling with the video card's refresh frequency? I know if its at a goofy setting it'll drive my eyes nuts.
Also, are you hydrated? Have you gotten enough rest or have you spent the night up late watching TV? That'll make a difference too.
Check with a doc. You may need glasses. If you do, its only to help and allow you to be more productive. Its your health!