1990 AL Bob Welch over Roger Clemens
Welch won 27 games--most in the majors--and had the best record in baseball. He also logged 238 innings of sub-three ERA ball. But his peripherals were rather pedestrian, and he was worth just three wins above replacement. Clemens was valued at more than ten. His ML-best 1.93 ERA was more than a full run lower than Welch's 2.95, which gave Rocket the best adjusted ERA (211) in baseball. Rocket also led the bigs in shutouts, HR/9 and K/BB ratio. Clemens would win again the next year, but he should have taken the trophy in 1990 as well.
1992 AL Dennis Eckersley over everyone else
Eck saved 51 games and was voted American League MVP as well as its Cy Young, but didn't deserve either award. He shouldn't have won MVP because nobody who pitches 80 innings is an MVP, even if he throws 80 perfect innings (which Eckersley did not). As for the Cy, well, there were several more deserving candidates. Runner-up Jack McDowell tossed more than 260 innings and won 20 games, but I would have gone with third-place Roger Clemens, who was worth close to nine wins. Rocket won the AL ERA crown (2.41) and posted the league's best WHIP and K/BB ratio. He also had the best ERA+ and most shutouts in baseball. Mike Mussina (8.2 bWAR, 2.54 ERA in 241 innings) was almost as good, but Clemens was clearly the league's best pitcher that year.
1993 AL Jack McDowell over everyone else
McDowell may have had the most wins (22) and shutouts (4) of any pitcher in baseball that year (on top of his 256-plus innings), but like Jack Morris he was more quantity than quality. Runner-up Randy Johnson rung up 308 strikeouts, almost twice as many as McDowell, and had a better ERA in just as many innings. An even better choice would have been Kevin Appier, who finished third despite accumulating 9.2 bWAR and winning the ERA title.
1998 NL Tom Glavine over everyone else
Glavine had one of the best seasons of his Hall of Fame caliber career, winning 20 games (most in baseball) with a 2.47 ERA in 229.1 innings, which was worth 6.1 bWAR. But he didn't lead the league in anything else, and generally speaking if a pitcher's only black ink falls in the wins department then he probably wasn't the league's best. Third-place Kevin Brown, with 100 more strikeouts and a better ERA in more innings, was clearly better. So too was Glavine's rotation-mate Greg Maddux, owner of baseball's best ERA (2.22), ERA+ and WHIP.