I'm swapping out 1/2 inch copper pipes and adding new valves in my basement. When I removed the old 1/2 inch pipe I looked at the inside of the pipe and noticed how dark it was. I stuck a paper towel in it and when I pulled it out it was dark brown. It made me thankful that I use water filters. My question is whether this is normal for the pipes ( they are probably at least 40 years old) or should I hire a plumber and change out all of my pipes for new ones. Thanks for any advice.

It's copper oxide. While at high concentrations, copper can be toxic, at levels found in plumbing, it's quite harmless to humans. Trace amounts of copper are required for good health.

Copper - Wikipedia, the free encyclopedia