Cyborg 002 is the father of Brendon Small
Jet Link had an affair with Paula from Home Movies
, which produced an illegitimate son with Jet's long, pointed nose and hairstyle.
The reincarnated 003 is pregnant with 001 at the end of God's War The ending states that even though 001 isn't present in the group shot, he's still there. Joe and Francoise are married in this new world and Ivan will be reincarnated as their son, since Francoise served as a substitute mother to him during the series proper.
Cyborg 009 is a Speed Force user
Think about it. It all fits. The Superspeed, the molecule acceleration in the God's War OVA's, the red and yellow theme? Cyborg 009 is either now, or will someday become The Flash of his world.
Cyborg 004 was fighting his Tethered
Albert Heinrich's doppelganger in "Man or Machine" was actually his Tethered clone, who had received cybernetic augmentation to mirror his upper world counterpart. Much like the other Tethered, Albert's clone was incapable of speech and driven by an implacable desire to murder his counterpart.