I scanned an old 8x10 inch glass negative. Looks awesome. Then I zoomed in on an object and I see moire patterns. I then rescanned, after placing a piece of paper under each corner of the neg. It did not help.
What can I do?
Would it make a difference if I scan with the emulsion side down?

Any chance we can get a peek at the scan results? =)

I only see the pattern in one area. The rest of the image looks good. At least I have not found any more patterns. As you can see, it takes a lot of zoom to find it.

That my friend looks like a finger-print. =)
Try wiping the glass negative down and scan again.

I added another closeup image (above). You can see that the pattern spreads out and the rings get very narrow and close together.
There are some obvious finger prints on the emulsion side but they do not show up in the scan. The pattern that I am asking about does not correspond with any finger prints. The glass is very clean at that spot.

Color moire is easy since it's a monochromatic, but value moire much more difficult. Unfortunately, your image contains both types.

What is recommended for cleaning the emulsion side of the glass negative?

Some scanner drivers have the ability to eliminate moiré patterns. Check to see if your scanner driver has a glossy/magazine setting. Scanners I've used in the past have such a setting in their drivers. I've never had to do it but maybe someone here knows of specific scripts or filters that can assist you after the fact.

For what it's worth, there seems to be two opposed schools of thought. There seems to be a majority that recommend that the only cleaning on the emulsion side of glass negatives be limited to dust removal using a soft sable brush and/or a blower brush like what is used to clean camera lenses. Having said that, I located this pdf article that seems to indicate that water and a wetting agent such as Kodak Photo-Flo can be useful. The pdf article gives the impression that the emulsion on the glass negative is relatively tough.

Regardless, I would carefully weigh the benefits of cleaning verses the possibility of irreversible damage. I am sure you are already aware of this but it bears repeating: Should you decide to proceed, test a small area before beginning a wholesale cleaning.

I just read a small bit about emulsion cleaning and it stated that although emulsion is usually quite hard and durable there are times when you come upon a plate that is not as well (fixed?). Anyway, it is possible to cause a situation where the emulsion flakes off.
I think I'll do a lot more learning before I touch the dull side.

I've had a quick search on http://www.hybridphoto.com for suggestions on eliminating moire patterns (Newton rings), but I think it would be better if you post your question to the experts there as they will no doubt have questions for you, and can probably advise on cleaning glass negatives as well.

If you scan the same image twice, with the negative re-positioned between the scans, does the moire pattern appear in the same place relative to the negative or relative the scanner (or neither)? If not the former then you may be able to manually align the two scans and perform some blending/masking to reduce the visibility of the moires.

I used to use negative cleaner. It's strong and works wonders, but is safe on emulsion.