Before I start the list I'm going to quickly run through a few more honorable mentions/could haves and briefly explain why they didn't make it.

Skins
I've not watched the second season yet, so I don't know where the show goes after an excellent first season. But I've heard Sid is leaving, so I've lost interest somewhat.

The Dead Zone
A fantastic show that struggles in its six season, becomes brilliant again and then gets cancelled without finishing its story. Lack of resolution is all that kept this show out of the Top 50.

The 4400
The predecessor to Heroes 4400 failed to reach mainstream audiences despite it's brilliance. It was a little too sci-fi. Also it was cancelled at the same time as The Dead Zone and as such also failed to resolve it's story.

X-Files
Honestly, it lost its way later on in the series. It became a victim of it's own successes. But I will watch the new movie as I'm fond of the show.

Flight of the Conchords
Funny, quirky and wierd with fantastic songs. I enjoy watching it but I don't think it's a classic... Yet.

Carnivale
2 Fantastic pseudo-fantasy seasons. It's let down by it's early cancellation which leaves it unresolved.

King of the Hill
I enjoy this, it's good fun. But I find it instantly forgettable after seeing it. Like the Simpsons really.

The Sopranos
I've not watched enough of it to be able to personally list it.

Supernatural
Heard good things, have the first season on my shelf. Haven't gotten round to watching it yet.

Criminal Minds
Excellent show, let down by the best cast member leaving (Mandy Patinkin)

Bones
Too much "crime of the week" not enough ongoing story/plot/metaplot. But it is very slick and fun.

Weeds
Enjoyed it, need to get back into it.

South Park
I used to find it funny. But I no longer do. The World of Warcraft episode was brilliant, but then again I hate WOW so that helped.

Moonlight
Note to self: Watch this.

Men in Trees, Dirty, Sexy Money, Chuck & Mad Men
Heard good things about all of these. Need to watch.

Stargate & CSI
Both of these Franchises I just cba with.

Veronica Mars
Got canned too early, like 4400/Carnivale/Dead Zone

Buffy & Angel
Liked them, then got bored with them as they failed to evolve.

Rome
Just cannot be bothered with watching this. Not sure why.

Pushing Daisies
I really tried to like this, but I couldn't manage it. I don't know why this is, I should like it. I blame the narrator.

Justice League Unlimited
It's brilliant and would be in the top 100. But I couldn't fit it into the top 50.

TMNT 2K3
I'm just fond of this show as it's a better version of the cartoon I loved when growing up.

Psych
It's fun, it's witty, it's clever. But I'm not convinced it's top 50 material.

The West Wing
On my must watch list after seeing Studio 60

Invader ZIM
This one very nearly made it on. But lack of resolution and not wanting too many cartoons in the list kept it out

Twin Peaks
I love this, but I've never managed to sit down and watch it all in order so I still don't really understand it. :D