I’m always looking for new ones.
These are my current collection:
www.seattlepi.com/fun/
www.nydailynews.com/entertainment/comics/index.html
www.creators.com/comics/cat-seeall.html
www.chron.com/apps/comics/showComics.mpl
www.overzealous.com/comics/index.html
www.comicssherpa.com/site/home.html
Got more?
http://www.dailyink.com/en-us/
The Comics Curmudgeon
You already mentoned gocomics and mycomics.
http://www.somethingpositive.net
Oops - read the OP wrong. Although the above are great individual comics…
Some comics are only available for odd periods.
This comic can only be viewed a month after publication http://www.meehancartoons.com/comic_view.html
This site wants you to pay, so they just show free the first 7 days of the month. But all their comics can be found elsewhere on newspaper sites. http://www.kingfeatures.com/
Although it’s weekly, Dr. McNinja cannot be ignored.
A deadly ninja, who also happens to be a doctor. 
And I almost forgot, the Dresden Codak
I see that the OP prefers lists with dead tree comics. 
If you fear encountering the adult fare that can show up in Webcomics the site to check is the Belfry:
http://belfrycomics.net/view/all
It includes helpful legends like “A” for adult “V” for violence and so on.
Clicking on the “most read” and “most subscribed” can point you to comics that are interesting, controversial, and yes, even some with explicit content but you are warned by the legends before you decide to check them.
Has comics.com gone white side up, or just having technical problems for two days?
They flaked over the holiday and then recovered, but died again today. This happens to most comic and also crossword sites. My guess is that the guy who does the task takes the holiday off and his schlub of an assistant was only taught how to update for a single day, not a full weekend ahead, and certainly not a holiday weekend.
And the painful part of Comic.com is that their latest “upgrade” does not let you back up the site to yesterday for all the comics together, you have to click the back button once for each title.
It is back up to date now.