Depends on what you value in a scarf. Wool is one of the most perfect fibers available. It is warm, lightweight, durable over time, and has excellent shape retention. Wool's one drawback is scratchiness. If you like wrapping a scarf several times around your neck right next to the skin i like I do, 100% wool might be too itchy for comfort. (Although some wools are softer than others.)
Alpaca is an excellent choice, as it is even warmer by weight than wool, and is heavenly soft. Alpaca's one downside is that it lacks the excellent shape retention of wool. Alpaca has decent to good shape retention, just not excellent. That, and it is expensive.
Personally, i don't much care for silk or cotton yarn for knitting. Same reason for both: they are fibers which have very little "give." They have hardly any stretch, which means they are harder to work with, and have poor shape retention in the finished product.
Blends of different fibers can produce a wonderful yarn. I made a friend a scarf and mittens set with a yarn made of alpaca, lambswool and silk, and it was so comfortable she wore it to bed in her draughty New England house.
I don't think one should use synthetics if knitting by hand. if you are going to invest the time, use a high quality yarn. Your time is the most valuable thing in the equation, so don't scimp on materials.
It really depends on what you are looking for in the finished product. Are you looking for a bulky scarf to keep you warm or a lacey scarf that is more a fashion accessory than a source of warmth?
It also depends on who is going to wear the scarf... check to see if they are allergic to any particular fiber. I spent time knitting a beautiful scarf with Lamb's Pride by Brown Sheep (a beautiful yarn for a soft, warm scarf), only to find the intended receipient was allergic to mohair.
For cozy winter scarves, I'm personally partial to alpaca. It is soft, beautiful and warm. There are also several alpaca blends on the market now, making it even more affordable to knit with.
For pretty "accessory" scarves, I love to knit with handdyed sock yarns.
I enjoy the wool and mohair blends yarn for crocheting things like scarves. The yard is softer and does not itch and it is warm and easy to care for.
Soft Mohair, is nice and some of the feathery yarns are very nice, like the ones seen the last couple of years selling in Wall-Mart. Wool is very irritating to many people, expecially around the neck. It has a tendency to stick in the skin.
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