These lists are always great for debate because, aside from everything else people can disagree on, there's no agreement on the fundamental question of what "top Blue Jay" means. Is it:
1. the best overall player to ever put on a Blue Jays uniform
2. the best overall player who spent a significant part of his career as a Blue Jay
3. the player who accomplished the most as a Blue Jay
Win Above Replacement is not a perfect stat, but it's a good starting point for discussion.
IF you go solely by WAR,
Clemens is at 140.3 for his career (compared to 66.8 for
Alomar, 64.7 for
Halladay, and 73.7 for
Frank Thomas). In other words, on the basis of WAR, Clemens is so far ahead of every other person who ever wore a Jays uniform (I can think of) that he would have to be the winner based on criterion #1.
But of course, apart from how you may feel about Clemens and PED, he only played two seasons here. I agree that Alomar would probably end being Sportsnet's pick. He would be a lot of people's choice if you go by #2. And yet, he actually only played 5 of 17 seasons in Toronto. Because of that, if you only count
WAR as a Blue Jay, Alomar only ranks 14th
If you go by #3,
Stieb, with 57 WAR as a Blue Jay, is #1 on a top 10 list that includes:
1. Stieb 57
2. Halladay 48
3. Fernandez 37
4. Delgado 36
5. Bautista 36
6. Key 30
7. Barfield 29 (how cool is that -- it matches his number)
8. Wells 28
9. Hentgen 26
10. Moseby 25
As great as Stieb was (and he was vastly underrated by his win-loss record), his placement has a lot to do with the fact that he played all but 4 games in a 14 year career with the Jays. For my money, balancing overall career achievement and what he did while playing for the team, I'd go with Halladay. His candidacy as the greatest Jay gets dinged because the team never did anything while he was here, but you can't blame a guy for the quality of his teammates, particularly one who only plays every five days. He carried the pitching staff and was almost always worth the price of admission when he was on the mound.
If I have to go with a positional players, I would go with Alomar. Delgado, and Fernandez as my top 3.