Amonia level, Nitrite, Nitrate are normal. PH level is about 7. I have a 40 Gal Tank with two filters and I change the water every week. There are 6 Goldfish (3 Common, 1 Comet, 1 Black Moore and 1 Chocolate Pom Pom). I did add parasite meds just about an hour ago. I feed them flakes once a day. This goldfish is
3-4 inches in length and is bobbing, flopping around the tank like he's (or she's) drunk! I have him in a large breeding net at the moment. What do I do? Should I leave him in the net?

One problem I have spotted straight away is you are overstocked.The size of tank you have is too small.Each comet/common requires 20 gallons of water and every fancy fish requires 10 gallons.
What symptoms are your fish showing to make you treat with parasite treatment.Exact reading for ammonia,nitrite and nitrate would be helpful as ammonia and nitrite should be at 0 in a cycled tank.
Water quality is probably your main issue for ammount of fish you need to water change a minimum of twice a week.I would do an immediate water change of 50 to 70%.See if any change in condition.Please answer as many of questions in box above it helps us help you better

I know I'm overstocked. I've been looking for an acrylic tank (72 Gal) but I can't find a company that will deliver to Maritimes (Canada). I've had the tank for about 3 years now and experience has told me that there might be something wrong internally, that's why I treated with meds - also a small case of panic over losing a pet! The exact readings of Nitrite, Nitrate and Ammonia are zero. PH is 7. I will be back shortly after I do a 50 - 70 % water change and let you know if there is any change in his beaviour.

As Blue has stated the overstocking is probably leading to the problem.
Now to try and help further.

It sounds as if the fish has some SBD issues. (swim bladder disease) You can read up on this.
Water issues will inflame this condition in fish. So working to resolve any water issues is a must.

I noticed that you said your nitrates were 0 is this true? If so you have a huge problem. It means the tank isn't cycled. Please clarify this asap.

Fasting a fish with SBD is a good idea. A good 2-3 day fast followed by peas for a couple days along with getting the water under control will help. Not cure it, but help it.

I've finished changing the water and observed my fish for awhile. He is still swimming eratically, but when he stops he floats to the top - swim bladder disease. I will not feed them anything for a day or two and give them peas and see what happens. I retested for nitrite and the levels are somewhere between 0 and 0.25 ppm. Unfortunately I used the last of my nitrate kit on the test where I stated the level was zero. But I understood that levels between 0 and 40 ppm were ok. And to keep the water oxygenated I use an airstone, which I understood helps keep nitrate under control. Since it's past 9pm here I will not be able to purchase a new kit until tomorrow. Would a live plant, say a water lilly, help with the nitrate levels?

Not sure where you found that using an airstone would control nitrates........but it doesn't. Nothing does but water changes. Plants "can" aid in helping but are not reliable to control them, they just aren't enough.
I would recommend reading up on cycling. In an established cycled tank nitrates are present, meaning above 0. Keeping them at a certain "safe" level is then required. 10-40 is ok. However fish with SBD often start having problems with anything above 20. Make sense?

Any trace of nitrite is not ok. It needs to be dealt with asap. Especially if the tank has cycled. While cycling you play a "russian roulette" with nitrites and hurthing the fish.

Hang in there we'll help you get it worked out.

Any news?

Heres a usful swim bladder link for you.

http://us.geocities.com/swimbladderhelp/index.html