I had a Canon Hv 10 go bad on me. The last footage that I took contained some nasty looking pixel artifacts. Mostly clear jagged pixels. Does anyone know of any software or tricks that I can use to remove those artifacts? Either HD or DV.

You could try masking out that area and putting something else underneath. Sometimes putting the same video slightly offset can work. to fill in the masked area.

I found 3 hours of footage with bad pixel artifacts. Sometimes as many as five per minute.

Ok, so you're saying most of the time there is no pixels but every now and then you get a bad frame????

The camera malfunction. Canon couldn't fix it. They replaced the HV10 with a HV20. Around 20% of the footage has horizontal clear pixels. The pixels appear as wide swashes running across the clips five to twenty frames in length. I have 3 hours of such footage.