To help keep your bag clean, always wear a full pajama set of some sort. Most important part is socks.
Going to bed barefoot is the second best way to grunge up your sleeping bag IMO. Best way to funk it up is to sleep nekkid.
I recommend a full change of clothes, so that you're not sleeping in sweaty clothes, these tend to go clammy and give me the chills.
For backpacking I have a seperate pair of sleeping socks to keep foot funk from touching my sleeping bag. I also recommend a wash down of sorts before crawling in to bed.
In really cold weather, a down vest or jacket can make the difference as well.