First 3 to come to mind for me were Barnaby Jones, Lost In Space and The Odd Couple.
I loved the theme for Northern Exposure, along with the rest of the soundtrack.
Twin Peaks
Tales from the Darkside (“On the Darkside” by Eddie and the Cruisers aka John Cafferty and the Beaver Brown Band)
And the Dougie goes to…Neal Hefti for The Odd Couple, The Bob Newhart Show AND Batman.
priapus
I believe when you said “Johnny Yuma” you actually meant the television show “The Rebel” starring Nick Adams as Johnny Yuma.
It was a great theme song done by the legendary Johnny Cash and sung to the tune of “Dixie”.
Johnny Yuma was a rebel, he roamed through the West …
By the way, did I mention I like the Hawaii Five-O theme song? 
Aloha
some of my faves have been mentioned already, but off the top of my head, in no particular order:
Rockford Files
MAS*H
Peter Gunn
and if you’re going to mention Peter Gunn, you must include
Courageous Cat And Minute Mouse
Hawaii Five-O
Night Court
Secret Agent
The Cosby Show ('84-'92) Season 4
Friends
Animaniacs
Tiny Toons
WKRP In Cincinnati
The Smothers Brothers Comedy Hour
Monk
Mad About You
George Of The Jungle
to name a few…
The Critic.
I’ve searched high and low for a full version of that song, but alas, it is no where to be found and may not even exist 
I second ***Boondocks. *** “I am the ballot in the box, the bullet in the gun…”
Angel
Firefly
Gummi Bears
(I have these on my playlist and play them often)
Children of Dune, not sure if that counts (miniseries)
and I hate the show, but I love the themesong:
Spongebob Squarepants
Good, nobody has yet mentioned Stingray (although the Mike Post, er, post, did cover it in general form.) Ditto for Law & Order.
I find it hard to believe, though, that none have mentioned The Equalizer, which I believe was penned by Stewart Copeland.
And as other have mentioned, The Rockford Files, Magnum P.I., Peter Gunn, The Saint, The Persuaders, Hawaii Five-O, The Greatest American Hero, The Twilight Zone, and too many others to mention. Heck, for some of these shows, the theme was the best part of the show.
Oh, and nobody mentions Monty Python’s Flying Circus?
Stranger
forgot to mention (after trolling through itunes)
Kids in the Hall
Gary Shandling
My So Called Life
Alien Nation
Earth: Final Conflict
Where in the World is Carmen Sandiego?
Charmed
Reading Rainbow
Everwood
not theme songs, but I love the songs from Buffy’s Once More with Feeling
and Phoebe’s songs on Friends, especially the Smelly Cat Remix
and not favorites but just find them amusing because they are so damn short (hijack - shortest theme songs?)
Lost
Will & Grace
Green Hornet was the best of the Jazzy themes.
Firefly had the best song.
I like Ghost in the Shell:SAC.
You mean the game show theme, or the animated show’s theme?
The Liberty Bell March by John Philip Sousa
Having an Average Weekend by Shadowy Men on a Shadowy Planet
Well, if we are going to choose theme songs written long before the show ever saw the light of day, perhaps the best of the bunch is:
Rossini’s “William Tell Overture”.
Who had that theme song anyway? That theme song?
Why, that was The Lone Ranger!!! Hiyo Silver … away !!!
(Yeah, it’s already been mentioned by glee and priapus but I just wanted to cast my vote in typical Lone Ranger style).
(Great show too. Always watched it as a kid).
Lots of great mentions, maybe I missed it but I didn’t see The Sopranos , one of my faves.
Rockford Files
BH 90210 (show I hated to like, but great theme)
The Facts of Life (ok, that was a joke, for those who remember it I should apologize for getting that crap song in your head)
All I really remember is trhat he always wore the same filthy clothes.C’mon man,the war’s over,buy some levis
the show that got me rumming around the house in a sugar enhanced frenzy was the CISCO KID
Blimey give us a chance. I think the UFO theme is cooler. Thunderbirds is up there too.
Yet another vote for the Rockford Files.
And anyone remember the theme for Sledge Hammer?
Lain
Inspector Gadget (How could no one have mentioned Inspector Gadget?)
Those of you who love the Peter Gunn theme should really hear the brilliant mix on the Sopranos 2nd soundtrack, Peppers and Eggs, of Every Breath You Take/Theme From Peter Gunn - every time I play this CD, I always repeat this track at least once!