After a week of testing, I’ve removed the small Project Wonderful boxes from the top left. They never brought in more than a few cents, but more important was the effect they had on AdSense. The AdSense ad unit under them didn’t generate a single click while they were there. The leaderboard (big banner) near them at the top of the page got far less clicks than normal, and made almost no money.
PigPog doesn’t exactly bring much money in at the best of times, these days, but at least it’s usually not too far off covering the hosting costs. Adding the PW ads, though, took it to the level of making almost nothing. I removed those ads, and total revenues shot back up again immediately.
At the moment, there’s still a PW ad at the bottom of each pager, but I may well replace that soon, too. PW has been a better experience this time than when I last tried, and I still like their model, but there just don’t seem to be enough general advertisers to make it work for a general site. Within their core area of online comics and crafters, it’s probably a different story.