The Tick/WMG

The Tick is in the same universe as The Venture Brothers and Dr. Horrible
This has already been suggested by Word of God (one of them, anyway), but to be more precise I think Dr. Horrible is in the same universe as the live-action Tick, while Venture Brothers is the same universe as the animated Tick. This isn't just for practical reasons, it seems to me that the moods and aesthetics of the series' involved just sort of mesh that way.

The Evil Midnight Bomber What Bombs At Midnight is the same person as The Muppet Show's Crazy Harry.
Not only do they look alike and share a love of explosives, but their laughs are also eerily similar.

Obviously, Crazy Harry went even crazier and moved to The City to try to make it as a supervillain.
 * That would explain why he was talking to himself about his shot as a supervillain.


 * And Mad Stan is his son.

Batmanuel, the mayor of Gotham City, and Richard Alpert are all the same person.
Richard has often left the island on important Others-related business and may have posed as mayor of Gotham for a time in order to obtain new contacts, power, and money. After Batman decides Gotham doesn't need him, Richard dresses up as his own bizarre parody to try and help out before eventually giving up and returning to the island.

The Tick and Codename: Kids Next Door take place in the same universe
No shortage of crazy villains.