OK More details...

My car is an Integra 94 LS.

When I left it sitting for a few weeks, it was on the (duh!) emergency brake all that time, which I am certain is not a good idea.

I checked for air pockets on the inside of the tires and found none. The tires are filled with air at their respective PSI.

I just drove it a few minutes ago for about 10 miles. I thought maybe the brakes had crystalized as a friend suggested, so I let them warm up and braked pretty hard a few times including using my emergency brake a couple times to see if the clunking would go away, but it was in vain.

I can feel the scrubbing in the pedal when I brake.

Interestingly enough, it does not appear to make the scrubbing when I am in reverse.

OK... now do you have any more ideas?