Personally I like this one:
P.S. Do not hotlink the cartoon without the site's permission please.
Another one from xkcd  http://xkcd.com/327/
I like this one: http://xkcd.com/149/
(Proper User Policy apparently means Simon Says.)
('Are you stealing those LCDs?' 'Yeah, but I'm doing it while my code compiles')
I have this one pinned to the wall facing the entrance to our office :) http://xkcd.com/303/
Not a cartoon per se, but still good:
This has actually happened to me. A boss mistook my resourcefulness in scripting for laziness. link 
UPDATE: link  to original. Sorry about that. http://dilbert.com/strips/comic/2005-05-29/
Of course, xkcd !
I knew it was true. XKCD #224 
"We lost the documentation on quantum mechanics. You'll have to decode the regexes yourself." http://xkcd.com/224/
Taken from Dilbert.com, Sept 12 2008  http://dilbert.com/strips/comic/2008-09-12/
Formerly from here . http://cowbird.110mb.com/43.html
I can't believe someone hasn't put this one:
Manager and programmer :
Didn't see this classic
I really like this:
Dilbert is the top favorite, but I've also really enjoyed the xkcd comics the last couple years. I've got a couple of those posted up in my cube... I try really hard to live by this one.
I'm guessing that this would probably never happen, as agreeing to the terms and conditions is more important than actually reading them (from the software publisher perspective).
Bob the cobol programmer. A classic.
One of my favourite :)
If all bugs were so easy to close.
Dilbert - Numbing
One more which I liked: No offences.. :)
how it works
Without a doubt...
("40% of OpenBSD installs lead to shark attacks. It's their only standing security issue.")
I like this one (found on lemonodor.com ):
Fax me some electricity, please?
I guess this isn't technically a programming cartoon, but it's one of my favorites.
This strip first appeared on Sept 17, 1995, back in the days when 28.8K modems, a 66Mhz 486DX, and a soundblaster card were state-of-the-art.
I worked for a start-up called Telebackup at the time and guess what we were trying to develop? Scott Adams must have sat in on one of the management/developer meetings.
Anybody in web development can appreciate this one...
Quite demonstrative of why metric based incentives and engineers don't go hand in hand.
It's not really a programmer cartoon, but as a programmer I regularly have to deal with people who think JPEG is suited for everything. If you don't know what I'm talking about, read this . http://en.wikipedia.org/wiki/Wikipedia%3aPreparing_images_for_upload#Do_not_save_diagrams_as_JPEG
John Martz has a blog entry  to go with this. http://www.robotjohnny.com/blog/ie6-denial-message-for-momentilecom/
While not specifically about programming per se....wanting to program games is what got me interested in IT in the first place....
anyway this one made me laugh so hard when I saw it!
Cloud computing - simply explained
Here's a new one from Dinosaur Comics :
This has made my year.
Some engineer out there has solved P=NP and it's locked up in an electric eggbeater calibration routine. For every 0x5f375a86 we learn about, there are thousands we never see.
Someone has to post something other than Dilbert and XKCD ;-)
direct link  http://miscellanea.wellingtongrey.net/comics/2007-09-03--the-software-development-flowchart.png
Bit old but still one of my favs:
Another great Foxtrot comic. Possibly the most incomprehensible-to-non-geeks comic to sneak into the newspaper funnies.
I love this one:
This is my everyday.
(it's how people feel)
Geek hero is new but good.
The 1337 set of comics from xkcd, starting with:
The very first bug bash  is great!
According to http://homepages.strath.ac.uk/~cjbs17/computing/binary.html author of this image is Chris Kania and original is at http://www.kaniamania.com/html/1190.html but the entire site is down at the moment.
Not a comic, but a must see for everyone The IT Crowd . http://www.the-it-crowd.ch/The_IT_Crowd_-_Home.html
Check this From Apple Desicion on APP.
Linux is evil:
Can't help but love it...
Made for grad students, but applies equally to programmers
This Is my favorit.
"Emacs Thumb" from User Friendly 
My favorite : Cloud of doom
The Agile methodology was first called extreme-programming, evoking images of dudes with baggy pants, skateboards and inappropriate body piercings coding the company payroll. One of the most controversial practices was 'paired-programming'. Scott Adams explains why... (from Jan 9-11, 2003)
a nice collection  http://plg.uwaterloo.ca/~migod/fun/
My all time favorite is probably xkcd's "Sudo make me a sandwich" comic, but there are SO MANY good webcomics out there that I thought I'd throw some others out for fun:
A co-worker pointed me to Sticks and Stones , which just got started pretty recently. It's sort of an xkcd ripoff, but there's some good stuff in there.
C++ forest 
(sequel to this ) http://stackoverflow.com/questions/84556/whats-your-favorite-programmer-cartoon/448085#448085
Hackles is (was) a great cartoon..
I can't believe 6 pages of answers and no one mentions the banana jr 6000 . How quickly we forget.
The other one I love and couldn't find the image for has the punchline "Failure Mr. Jones, is hardly original. Now sit down."
Also from the Bloom County strip. http://toastytech.com/guis/bananaad.gif
makes me lol
link  http://xkcd.com/413/
I didn't see this one which is one of my favorite xkcd :
(His books were kinda intimidating; rappelling down through his skylight seemed like the best option.)
Hello my favorit is this one
I'm going to show my age with the this 1993 classic: On the Internet, nobody knows you're a dog. 
This one  hasn't been here yet. I would post it, but it's a little too big a picture. http://www.hanovsolutions.com/resume%5Fcomic.png
What?! No PhDComics? Check this out :
Remember this was 1997!!
Also read the following strips... Hilarious! http://www.phdcomics.com/comics/archive.php?comicid=13
Not technically programming related (coz almost all of them are already covered)
A very recent Dilbert one:
not directly something about programming, but i guess every programmer knows flowcharts xD
Edited for grammar :P
which language is he using? (or which company is he working for?)
Could have happened to me (as an UI designer...)
Lately I started reading Geek Hero Comic. My favorite parts so far:
(guess you have to work on sev zero bugs to get this one)
This is something I found reading about anti-patterns.
Offtopic, but necessary:
I can't help but notice a large amount of hotlinking of these images.
Golden Rule, people :(
This is old, I'm totally not sure about the permissions and I'm ready to remove it.
So anything on XKCD or Dilbert... WHO would have guessed!
I like these ones (link) ...
.. but it could be because I wrote them myself. http://gandolf.homelinux.org/~smhanov/comics
I read this yesterday... made me laugh...
I think the IT consultant's image is the best:
(linking because the picture's pretty big) http://eviljaymz.com/files/whypeopleseemtohavefreetime.png
LabVIEW programmers would write it this way...
Ten reasons you know you're living in 2009
Just had to put this here
From here  http://www.implementingscrum.com/section/blog/cartoons/
I love this one! And it all started here:
Not a comic, but it should be! http://rads.stackoverflow.com/amzn/click/0764543792
From InkTank.com  http://www.inktank.com/archives/AT/index.cfm?nav=148
Link fix for InkTanks " Debugging is a state of mind "
(can't comment - low reputation) http://www.inktank.com/2001/01/22/01222001/
For an Agile shop ... THIS is fantastic... As a dev, it just speaks volumes.
Great Fun: from Implementing Scrum  by Clark & vizdos.
Not really a programming cartoon. But I think (some) programmers go from enthusiastic newcomers who want to crash it out with technology and become rockstar programmers end up as the cynical manager types. A little bit like this cartoon about lawyers. From the Queen's Counsel
I just love Wulffmorgenthaler.com:
Howdy, this is my favourite. (Also displayed in my office!):
Was I can do stackoverflow in a weekend  the inspiration for this cartoon? http://blog.bitquabit.com/2009/07/01/one-which-i-call-out-hacker-news/
From Bug Bash :
We've got a clever tester now -What do you mean?
He's found bunch of stuff... A funny symbol there, a weird key combination here. He's real good
But sometimes... I really want to smash his face
Link to site: http://bash.org.ru/comics/20080111 http://bash.org/
I don't know about my favourite (xkcd and Dilbert are the obvious candidates, or course) but I found Mandatory Fun quite disappointing (sorry Alex, I really do believe that The Daily WTF  is one of the best sites for developers out there in the 'net, and I hope the comic will stand up to expectations sooner or later). http://thedailywtf.com/Default.aspx
Geek hero is new but good.
Tragically, my favorite cartoon is too old to be on the interwebs.
It's from Datamation. (Remember Datamation?) A man is sitting at a desk. There are bits of electronics everywhere. Rubble is strewn into every corner of the room. His face and hair are singed.
He is thinking "It's never done that before."
HAI CAN HAS STDIO? I HAS A VAR IM IN YR LOOP UP VAR!!1 VISIBLE VAR IZ VAR BIGGER THAN 10? KTHXBYE IM OUTTA YR LOOP KTHXBAI
Taken from :http://lolcode.com/ KTHXBAI!!
This is my personal favorite... and the name of all my alpha releases!
original link  http://www.phdcomics.com/comics/archive.php?comicid=1197
This  would be the better link .. http://www.projectcartoon.com/
The Contiki Strip
A comic set in a small Norwegian software company. All text in English. Check it out at http://contikistrip.kjempekjekt.com
Check out Shortminds.com  for more http://www.shortminds.com
“In addition, Professor Hopp has discovered a drug that eliminates the human need for sleep.” -- Andrejs R. Strikis ’62
I've had this cartoon, originally published in the Harvard Lampoon, on my bookshelf for more than thirty years.
I wish I could find it: Some suit is doing his drive-by management of the dev team saying "You guys start coding. I'll go find out what they want."
How about a math cartoon ?
Babbage and Lovelace Vs The Client
Includes historical notes
I like http://xkcd.com/297/ personally.
I liked the O'Reilly book Evil Geniuses in a Nutshell  http://rads.stackoverflow.com/amzn/click/156592861X
This is my favorite IT Crowd moment: You Tube Link . Oh, and the smoking room storyline in series two.
Manageability  http://www.my25percent.com/2008/09/manageability.html
This is from Steve Yegge talking about the verbosity of Java . http://steve-yegge.blogspot.com/2006/10/egomania-itself.html
Waiting for Bob
It's not exactly a programming comic, and it's been on "hiatus" since 2002, but some of the stuff holds up well. Lots of pop culture references, albeit dated at this point. I'm hoping for a return, but alas.
in which we discuss the philosophy of computer science and programming architecture by the seemingly-defunct Standard Out :
For those who have worked at Accenture www.bigtimeconsulting.com has some awesome ones...
Here are just a few:
Bold New Changes 
Hit and Run 
Tech Support 
Quitter  http://www.bigtimeconsulting.com/?toon_id=85
Test Driven Development (TDD) Smiley:
I liked it very much :)