Red cookies are more... random than the standard brown ones. Sometimes, you can get clots or ruin, and sometimes "elder frenzy" - a x666 bonus for 6 seconds.
Now, what should I do? I'm at a point where it will take almost 99 hours to earn the next cookie upgrade at the current rate, my next time machine will cost about 2 trillion, cursors no longer return investment so are only good for the achievement. The only plausible upgrade is
"Elder Pact" which frightens me a bit. It's even got a note saying "this is a bad idea"
Red cookies have a much higher chance of starting a cookie chain, which will net you over seven trillion cookies.
Getting Elder Pact will make it to where you only get red cookies, and will give you access a new achievement (more milk for the cats); nothing bad actually happens.