Ed's early tones sit at the top of the hill for me. I'm also a huge fan of George Lynch's various tones over the years. Greg Howe's early tone is sort of a cool hybrid of both those guys.
I saw Yngwie a few years ago and he had a killer strat/marshall tone.
I admire Satch as a player but have never really liked his tones. I got the G3 dvd not long ago and his tone on that is just awful. Vai has a very unique sound, but I liked it better on the first Roth record than anything he's done since.
Not a fan of Petrucci's tone. Sort of a more metal Morse tone. Morse is another player who is amazing but whose tone doesn't do it for me, though I saw him recently with DP and he sounded better than I thought he would.
As for the worst tones of the shredder era, maybe early Richie Kotzen (he REALLY got his act together later though) or Jason Becker.