From a distance runners point of view,If you can't manage 50 free standing squats or 20 press ups,then whats the point of doing weighted squats or bench presses?
If free exercises become too easy then you can make things more difficult by for example,elevating the feet during press ups or using single leg squats(hold onto something or you fall over :-)
I didn't mean to jump too heavily on your earlier point Popsider.It is just having spent many years of my youth training in gyms, I have seen people literally carried out on more than one occasion after piling too much weight on the bar.
I also would say that heavy squats are a big no no.It is much easier on the legs to employ exercises such as leg presses,leg extensions and hamstring curls.It is important to train both the quads and hamstrings,as neglecting one in favour of the other can lead to running injuries.
I must agree with you on the subject of free weights v machines.Whilst it is not always possible to use free weights(as with the above leg exercises)you should try to use them.
A machine allows you to move the weight in a pre-determined line.This line may not be one which works the muscle group through a full range of motion.You may also without even knowing it be pushing harder with one arm/leg,this can cause an imbalance.This may not be too important for general conditioning but can cause problems for runners.
I would suggest wherever possible,that dumbells by used for the upper body and single leg exercises for the lower.