Oh my god, I remember watching that as a kid. It comes back every now and then on reruns, and I think it's on Teletoon Retro as well (for Canadian viewers at least).
The part of the series that always sticks out in my mind is the four episode arc when they are fighting the super-virus Daemon. That, in my opinion was the peak of the series' greatness. That was near the end of the series I think. Though, having Tony Jay (the voice of Shere Kahn in Talespin) voice the villain Megabyte was also very sweet.
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The part at the very end of the series, when Megabyte returns, badder than ever, was also sweet. But they left us with a major cliffhanger too!
