Ouch, I'm really sore. Should I take a break for a while? How long? I was in to cycling quite a lot in high school,  but was unable to and/or really lazy in college. 

I've been getting back into cycling lately, doing a 65 miler two weekends ago, a 25 last weekend, and a 45 yesterday, in addition to biking to work (about 3.5 miles up a large hill in the morning, the same distance almost without pedaling on the way back) 6/10 days of those weeks.

Woke up this morning and I'm really really sore everywhere. Am I doing something wrong? Do I need to just "cool it" for a couple of days?
First off, if the soreness is such that you feel painful stabs when you move/stretch the muscles you definitely should rest for awhile (at least several days, maybe up to 6 weeks), and perhaps should see a doc.  This can be a sign of tendinitis, muscle pulls, or a muscle disorder, and continuing to exercise in such conditions can lead to permanent damage.

General soreness/stiffness, on the other hand, is believed to be caused by microscopic muscle injuries that, as they heal, tend to strengthen the muscles.  For such discomfort you need to take is easy for a day or two, until the soreness/stiffness abates.  However, moderate exercise (well below your max effort) to keep yourself limber is often advised.