YSB is Sudbury
YFB is Iqaluit (formerly Frobisher Bay)
YOW is Ottawa
YQB is Québec
YSJ is Saint John, NB
YTS is Timmins
YHU is St-Hubert
YWG is Winnipeg
YLT is Alert
YGP is Gaspé
YBG is Bagotville
YMM is Fort McMurray
YKA is Kamloops
… So they’re not all that bad. Some of them are totally nonintuitive, obviously. 
I couldn’t find any explanation for Toronto’s YYZ code, but I did learn that, according to this page, the Rush song “YYZ” is taken from that airport code (Rush is from Toronto).
Niigata Airport (Niigata Kuukou), is listed as KIJ. I have heard a few different reasons for this, but none of them have really seemed like anything more than WAGs.
ETA: The only part of the code I am pretty certain about is that the J is short for Japan. The final J seems to be fairly popular among regional airports in Japan. KagOshima Airport is KOJ and HIroshima Airport is HIJ.
This thread has prompted me to email the airport staff and ask them for the final word. Here’s hoping they’ll have something to tell me soon.
Also, Port Columbus International’s code is CMH, which is not totally counterintuitive, as it does have a C and an M. The code actually comes from an older name for the airport, which was Columbus Metropolitan Hangar. Several of my friends from the area refer to the entire city as CMH in internet shorthand, which I’ve always considered rather obnoxious.
Oh, I just thought of another one:
Chubu Centrair International Airport (Chubu Kokusai Kuukou) has the code NGO which is again a throwback. The airport replaced NaGOya Airport when it opened a few years ago. I don’t know if this really counts, though, because you can still at least guess the location by the name and I still hear plenty of people refer to Chubu Centrair Int’l as Nagoya Int’l.
Louis Armstrong New Orleans International Airport is MSY. It was previously known as Moisant Field but that isn’t the origin of the code. It is named after the previous tenant of the property, the Moisant Stock Yards.
Spokane International Airport (Spokane, WA) - GEG 
I came into this thread to suggest ORD, but your OP beat me to it.
:rolleyes:
Right on, Bubba! Excellent post!
Used to be known as Gieger Field. Spokane Airport - Wikipedia
I used to have a page bookmarked that had a explanations of many of them, but I lost the bookmark and wasn’t able to locate it via google-fu.
This seems to be germane to this thread. It’s a general explanation about airport identifiers, with some explanations included:
Just found these articles that explain some of them:
http://www.gonomad.com/traveldesk/0505/what_airport_codes_mean.html
http://www.skygod.com/asstd/abc.html
addtl: Rocket Surgery just beat me to the punch.
I detect…sarcasm. WHYYY???
You detect wrongly. That was sincere praise. One of the funniest posts of the day for me. Not quite as funny as another I had already anointed as Post of the Day in another thread. So I had to use another way to let you know I enjoyed your humor.
Actually, both of you were stealthed out by TJVM in post 22 
Saskatoon is YXE, but I have no idea why.
Regina is YQR, which is understandable (Queen Regina)
Williamsport, PA’s airport has a code of IPT. Not WPT, IPT. I’m guessing WPT was already taken by someone else.
Except that there was never a person named “Queen Regina”, and it’s a phrase I can’t imagine appearing in any other context – even if ‘Regina’ is Latin for ‘Queen’. More likely the R has significance, but the rest of it comes from being named as part of this series:
CYQA Muskoka
CYQB Quebec Jean Lesage Intl
CYQD The Pas
CYQF Red Deer Industrial
CYQG Windsor
CYQH Watson Lake
CYQI Yarmouth
CYQK Kenora
CYQL Lethbridge
CYQM Moncton
CYQN Nakina
CYQQ Comox
CYQR Regina
CYQS St Thomas Muni
CYQT Thunder Bay
CYQU Grand Prairie
CYQV Yorkton
CYQW North Battleford
CYQX Gander
CYQY Sydney
CYQZ Quesnel
Reagan National, formaerly Washington National, is DCA. This is recognizable, although it’s never had “DC” in its name. Washington Dulles International is IAD, which maybe means International Airport, Dulles. I think Houston’s main airport is IAH, which maybe follows the same pattern.
The airport in Newark NJ is EWR, IIRC.
Why LAX and SFO, instead of LAO and SFX?
CID Cedar Rapids Iowa airport
LAX was previously known as LA when two letter codes were used. When the transition to three letter codes was made, they tacked an X on to the end. See also: PDX.