His nerd jokes were occasionally actually really good. When they weren't, they came across with the air of "Fuck you, I'm not putting these comics online for you." Occasionally he'd hit upon a nice riff with his heartbreak comics, too, and his whimsical outlook towards life was a lot more sincere and less forced. Then he homogenized, began repeating joke concepts, and started spitting out a lot of derivative work, with only the occasional truly clever idea. It's never gotten worse than mediocre, but it's very frequently mediocre.
I guess what I'm trying to say is all of you should read Achewood instead. The nerd jokes are better (http://achewood.com/index.php?date=09232002), it's funnier than any comic I've ever read (it's the comic that topped Calvin and Hobbes after seventeen years on the top of my list), and it's a real start-up, selling monthly premium updates rather than relying on any advertising whatsoever.
It sort of amazes me that so many people can be fans of discomfort humor and missed-context humor (like in "The Office" or "Parcs and Rec") and yet when it is applied to something friendly to them they flip out. We all agree the outrage over this silliness is part of the fun in this project. You could probably apply this same joke to ANY webcomic if you have the right tone. If you want to see someone doing it wrong, check xkcdsucks.