If I remember correctly the logo and the agreement with Commodore behind its use
Wayne Hunt got Commodore's permission to use the amiga.org domain in 1994. The logo that is currently in use was introduced much later: it features the BoingBall and the red diamond, elements introduced by ESCOM. A quick check using the Web Archive suggests the current logo design started showing up in 2001.
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were the main asset A-EON wanted
Obviously. They started using the amiga.org-Logo on completely unrelated commercial products like the Enhancer bundle pretty soon.
If I remember correctly the logo and the agreement with Commodore behind its use were the main asset A-EON wanted when it approached Wayne to purchase amiga.org. --
Partly right. Wayne was looooong gone when that happened. A-EON bought it from DiscreetFX.