The liquid that fills the inside of the entry plug. Viscous in nature and having a blood-like odor, when charged by electricity its molecular arrangement is altered, allowing L.C.L to perform a number of functions such as mentally linking the pilot and the Eva, supplying oxygen, and providing both physical and mental protection to the pilot. This same L.C.L also fills the lowest level of Terminal Dogma where Lilith is kept. Various interpretations have been circulated such as that "L.C.L" is the abbreviation of "Link Connected Liquid", but what it appears to be is the actual "soup of life".

(Translator's Note: The Evangelion: Death and Rebirth Movie Program (Sp. Ed.) states clearly that "L.C.L" is not the abbreviation of "Link Connected Liquid".)

Source: The End of Evangelion : Glossary contained within The End of Evangelion - Theatrical Program.

In response to Regulus's conclusion: I think LCL originated from Lilith, though I don't know if blood is the appropriate term. It clearly has some of the properties of blood (in particular the smell), but it's doesn't look like blood, and there is a whole sea of it there down in terminal dogma, so I don't think it is vital to keep Lilith "alive". Of course this begs the question of how Lilith exists without a soul (her soul is in Rei), but that's such a big topic I don't think it's a good idea to go into here (msg me if anyone wants to discuss it).

LCL stands for less-than-containerload. So if you have an LCL shipment, you'd probably want to ship it with an NVOCC.

As you are not the only one that wants to ship less than the full container, the NVOCC will throw all your stuff and the other people's stuff in and charge all of you. But it would usually still be cheaper than sending out half a containerload.

Regarding LCL in Neon Genesis Evangelion, my conclusion was that it was Lilith's blood.

Evidence (Warning, SPOILERS):

Episode 7: Shinji Ikari: "Keeping the Earth safe. That's what Eva's for. Come to think of it just, what is Eva? This entry plug smells a lot like, blood. But I feel so comfortable and relaxed here. Now that I think of it, I don't know anything about it."

Episode 15: Kaji and Misato stand in Terminal Dogma outside a (rather imposing) door marked "LCL Plant".
Kaji: "...But you should know that the Commander and Ritsuko are keeping something from you, too. And this is it!"
(He swipes his ID card and the door opens, revealing a crucified giant that also happens to be missing its legs and lower torso. From these wounds flows a yellow ichor, filling the huge chamber.)

Episode 16: Shinji, trapped inside the 12th Angel, says: "The water’s getting cloudy! The purification system is breaking down! It smells in here! Blood! This place smells like blood!"

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