Let's say someone wants to gain muscle size as their overall goal... What negative and positive effects will running have? What can be done to minimize any negative effects or should running be avoided all together?

Here is what I'm thinking...

Positive:
-Improved vascularity
-Cardiovascular health
-Burn fat
-Mental clarity
-Remove waste/toxins from body

Negative:
-Burn hard earned muscle
-Over training possible
I'm running out of negatives are there more? It seems that the positives outweigh the negatives at this point...

If your overall goal is increased muscle I wouldn't recommend long distance running. Instead try some sprint intervals. You can go to your local track or run on the street in front of your home. Sprint 20 yards, walk back. Then 40 and walk back. Increase up to a 100. Compare the body type of Olympics sprinters to Olympic marathoners and you can see how sprint intervals are more conducive to holding onto muscle.
CR

Definitely a good contrast and compare with the sprinter and marathoner. I'll probably throw in some sprints here and there just to stay in good cardio health. The best time I'm guessing would be after a workout or on off training days.

It's all going to be depending on two things: Genetics and diet. I do know some pretty thick distance runners. You can teach a sprinter to do distance but you can't teach an endurance runner to be a sprinter (muscle twitch factor only).

If you're going to do the distance, up the cals and carbs, preferably, potatoes. I hated running more than 2 miles, but a few years back, I got into the best physical shape and actually got into contest shape ACCIDENTALLY! Timing of carbs was and is important.

I say to try it and see if you're losing strength. If so, up the cals. I feel it worked for me, it just may work for you.