Hamstring insertion tendonitis (on inside, back of knee, sometimes below the knee)... all winter 2008/9, then after September 2009... working on it by improving strength (going well) but running significantly decreased while it gets sorted out.
Update, April 2010: No real problems with this for a while, won't call it 'over' cos its the kind of thing that comes back, and might do again when do more running training again.
When I had these problems I was a bit on the thin side, I had hardly any muscle or strength in my legs! Had no problems with this for ages now, am much stronger. Won't let it happen again.