I'm not a doctor but the ones I spoke to were clueless, so I had to work it out myself. There are a number of possible causes, according to the internet that is, which I'll list to save you a lot of research on google. Trial and error will show you which one applies to you.
1) STD: You should know if this is likely, get yourself tested.
2) Prostate infection: I'd have thought you'd know about this as well if you have one given the other problems it can cause just going for a pee. These can be chronic apparently, as it’s difficult for antibiotics to get in. The home remedy some people seem to recommend after giving up on the medical profession is 'milking' the prostate with a finger. You get the gist and can lookup the procedure yourself. I would have thought ejaculating a lot and doing exercise would also help.
3) Prostate cancer: I wouldn't worry about this unless it's brown, which would indicate blood. If you've just done a lot of strenuous exercise, that's probably the cause. See a doctor anyway.
4) Dehydration: I don't see how but some people said it. Drinking a lot of water just made me pee a lot.
5) Urine in the semen: This may be left in your tubes after you go and mixes in when you ejaculate. I'd have thought this should be cleared out by pre-ejaculate, but I don't know. I suppose you could test it by drinking a lot of water until your urine goes clear or do pelvic exercises to strengthen your muscles to help expel everything.
6) Lipofuscin: This is what gives semen color and it’s essentially crud left over from the processing job done in your liver when it cleans out and breaks down stuff from your blood. Why it ends up in the seminal fluid is a mystery to me, but there you are. When things are fine there isn't enough there to see it.
As you get older, you get more of it as the liver ages (its an age related pigment) so semen tends to turn more yellow (Lipofuscin apparently builds up in the brain too and may have something to do with Alzheimer’s). Having eliminated the other options, it’s then a question of what is causing the lipofuscin, and I reasoned its either something the body needs, which it isn’t getting enough of like vitamins, or something harmful it’s getting too much of which brings me to…
7) Alcohol: In case you didn’t know, poisons -- like alcohol -- are broken down in the liver and this is what I eventually concluded was the problem. It's easy enough to test. Take a month off the booze and see what happens. I say a month because semen production is a long process and effects will take a while. Ask yourself if you only drink at the weekend is it better or worse for the next day or two. Apparently, Acetyl-L-carnitine also helps flush lipofuscin from the body. This is produced by strenuous exercise.
Of course, it could be something to do with booze that isn't lipofuscin at all but thinking like that got me my answer. Cut out drinking and start exercising. Who knew?