Basically listen to your body. If I feel like crap, I start out with stretching. If I still feel like crap, then I might do a short run or other exercise (weights, intervals, stretching). If I feel better after stretching, then I may go for a run. Sometimes, I run while feeling like crap and feel better as I get warmed up.
I will run with a cold - I think that I've had one for a few weeks and it's tapering off now. I don't go running if I have the flu.
4 x IG Prestige MP, 70 cm, 376 grams, 386 SW, ALU Power @54, Prince Syn Gut 16 @58