Naruto and Gundam Wing were both popular and good (as well as groundbreaking for the block), Month of Miyazaki was chosen because it was the last great Toonami event, Outlaw Star was just cool (as the list said), and Justice League was the culmination of the DCAU (aka the universe that made comic book cartoons awesome again) done in excellent fashion.
Dragonball, Megas, IGPX, etc. may have made the list had we done a Top 10. As for DBZ, Sailor Moon, etc. they premiered in the 90's and were thus ineligible. Same reason why you won't be seeing PPG on the upcoming "Top CN Originals of the 2000's" entry.