Are you referring to the muscles in your neck and upper back or your windpipe?
At times you may get a crimped windpipe when practicing headlock escapes or when chokes are applied a little too enthusiatically. What I did was to avoid any compression on my neck for a week or two and the crimp in my wind pipe went away.
For the neck and shoulders, as stated in other posts, there are exercises around to strengthen the neck.
In Judo, we would warm up the neck by getting all fours an put your head on the mat (as if you are assuming the drop drill position). We would then roll forward and back on the top of your head to stretch the neck. Go very slowly at first and gently test the limit of your flexibility. As your neck and shoulders become conditioned, you can keep you head down and elevate your hind quarters. Eventually you will be able to support your weight fully with no support from your hands. You can also take the exercise further by then walking your body in a circle (like the break dancers).
Hope this helps