For runs below freezing, I swear by my merino base, light fleece, and a wind shell. It's the only thing that's worked for those early Oakland mornings when the wind comes right off the bay. I did a hard interval workout once in 28 degrees and stayed warm but not sweaty, so I didn't freeze when I stopped. Best to start light and add more as you go.
After years messing around in the mountains, this is the layering combo that actually works: a merino base, light down midlayer, and a windproof shell. We tested a bunch of options on Mount Blanc, and this setup won, especially near the windy summit. I remember one early morning climb where I wasn't sweating at all and could quickly adjust my layers. Honestly, the trick is having layers you can vent or shed easily while you're moving.