2003: 86-76 (87 win pythag)
2004: 67-94 (71 win pythag)
2005: 80-82 (88 win pythag) - Halladay broke his leg and missed half the season that year
2006: 87-75 (86 win pythag)
2007: 83-79 (87 win pythag)
2008: 86-76 (93 win pythag) - had a better run differential than the Rays who won the division that year, and 4th best in MLB
JP built some good teams that were stuck in a division with two powerhouses, one wild card, and unbalanced schedule. He wasn't great or anything, but he was a solid GM.
If he knew how to draft at all, we'd remember him a lot more fondly for his work (his mouth is a different story, he and Keith Law were a match made in heaven, two douchebags working together).