Many games have an intro, and I think, that it can be a good way to get into the story, but sometimes the intro is so unessesarily looong (and/ or bad), that you just want to skip the rest, but of course it's unskippable.
But how long can an intro be? As far as I know Yakuza 2 has the record- you will have to wait more then half an hour before you get any gameplay.
On the other hand Final fantasy tactics advance didn't give me any chance to save untill about 40 minutes into the game.

well dunno about the longest game intro but the most annoying on is civilization 5 and the fact that it is impossible to skip it lol

Metal Gear Solid 4 has a pretty lengthy intro from the time you choose New Game to the time where you actually control your character, which leads immediately into another long cut scene.

I also remember Xenosaga 1 having a ridiculously long intro.

Don't know, i stay away from movie like games.;) Yes there is, just change SkipIntroVideo's value from 0 to 1 in UserSettings.ini, burried in %USERPROFILE%/My Documents/My Games/Sid Meier's Civilization 5/ folder. ;)

Metal Gear Solid or Yakuza games probably.

What about that old Panzer game?

Eternal Sonata is my personal pick. 45 minutes of unskippable generic JRPG-boredom, unless I counted it wrong.

And I still love the game like no other.

I was going to point out that new Ghostbusters game (the very recent shoddy one) has something like a 20 minute intro according to RPS. But Xzaril has plainly trumped that already.

The Shin Megami Tensei and Persona series tend to have very long (interactive) intros.

But it's awesome. :P
And you can actually skip first four minute CGI sequence.

Gran Turismo 5 maybe? It actually has two (long) intros joined together.

Persona 4. Holy crap. It seriously takes around 4 hours until the game truly begins. Persona 3 maybe 20 minutes.

Warhammer Dawn of War and Warhammer Dawn of War 2.
Both have long intros, but they are great and not annoying at all.
I watch them almost everytime I play the game.

Panzer Dragoon Saga (oh god I love that game) ?The first FMV was about 15 minutes long.
Tactics Ogre Let us cling together intro was pretty long. Mana Khemia on PS2 had a long intro too.
And the intro of Valkyrie Profile was about 40 min.
EDIT: If I remember well, the intro of Wachenroder, an underrated tactical on Saturn (never released out of Japan) had a quit long intro