Allegedly, Arthur Leigh Allen was eliminated as a suspect because his fingerprints didn't match those found at the scene of the Paul Stine murder. He still is such an intriguing suspect.
This is one that always interested me.
In 2009, a former lawyer named Robert Tarbox (who, in August 1975, was disbarred by the California Supreme Court for failure to pay some clients)[103][104] said that in the early 1970s a merchant mariner walked into his office and confessed to him that he was the Zodiac Killer. The seemingly lucid seaman (whose name Tarbox would not reveal due to confidentiality) described his crimes briefly but persuasively enough to convince Tarbox. The man said he was trying to stop himself from his "opportunistic" murder spree but never returned to see Tarbox again. Tarbox took out a full-page ad in the Vallejo Times-Herald that he claimed would clear the name of Arthur Leigh Allen as a killer, his only reason for revealing the story 30 years after the fact. Robert Graysmith, the author of several books on Zodiac, said Tarbox's story was "entirely plausible".
https://en.wikipedia.org/wiki/Zodiac_Killer#Public_speculation
He fits with the theory that this was someone who spent long periods of time away from the Bay Area, perhaps someone in the Navy (because of the location of the Stine murder). But who knows?
There some others too. (And there are some ridiculous speculative suspects too, like the Unabomber). I wish we could solve this one in my lifetime.