God, that was awful.
First, I wanted to point out how they're similar, and how I justified comparing them. Draft position was the easiest: Bestiaire has them back-to-back at #32 and #33 overall, with Corpsejack holding the slight edge. They're both creatures, they're both multicolored, and most importantly, they both offer a bonus to particular deck archetypes.
Wayfaring Temple fits squarely into a Selesnya deck. Selesnya lives on amassing an army of creatures, and Temple helps with both creating creatures and benefiting from them. Corpsejack meanwhile is a pure fit into a Golgari guild because of his mana, but also gives a bump to the Rakdos keyword of Unleash, adding a second +1/+1 counter on unleashed creatures.
Corpsejack's bonus is easier to proc. There are dozens of easy ways to stack counters on your creatures, from Dead Reveler to Slitherhead to Sewer Shambler. And if you're splashing some white, Common Bond turns into a titan of a card. By the same token, though, the immense value of Corpsejack's passive ability makes it risky to swing or block with him. That means a 4/4 creature is going to be sitting on the sidelines for part of the time. Rough deal.
Populate is a stronger mechanic than dropping an extra +1/+1 counter, but the method for getting it to hit is considerably more difficult. Obviously if the opponent has no blockers, that would help, but that's not a likely scenario for a 2-color 3-drop. So you're stuck with a couple situations. First, that you can make your guy bigger than your opponent's creatures, and that he'd rather keep his guys and let you populate rather than block your guy (not super common).
The other option would be to use other cards to create ways to get damage in. Detain helps, so you'd definitely want Azorius Arrester and Azorius Justiciar in your draft. You can also use trample to get in, using Selesnya Charm or Chorus of Might. But truthfully, you can't really count on those cards coming through. So, more likely, you're looking at Wayfaring Temple as just being a */* creature who can use some of those populate cards as combat tricks (like Eyes in the Skies turns into a +2/+2 instant bump). Definitely has value, but the secondary function of populating on combat damage isn't likely to come into play very often.
In the end, I'm taking Corpsejack. While Wayfaring Temple creates some interesting possibilities, it seems like the kind of card that seems really good, but comes up short when you're playing against an actual person with his own plans and cards and removal. Corpsejack helps a lot of cards get better, and as a 4-drop, it's not the kind of card you'll find yourself waiting forever to play. I can see Wayfaring Temple being a great treat for a deck already firmly in Selesnya, but I can't see moving into Selesnya for it. Corpsejack, I could see moving into Golgari for.
Joe's pick: Corpsejack Menace