Lilith
Presumably the second Angel is Lilith, the Angel held by NERV deep within terminal Dogma and mistaken by Misato and Kaji for Adam.  Little is known about Lilith and where she came from, however, the seventeenth Angel, Kaoru, refers to humans as lilims, implying that Lilith is humanity's mother.  The room Lilith resides in deep within terminal Dogma is actually NERV's LCL, Link Connection Liquid, manufacturing plant, it is here that Lilith hangs nailed to a large scarlet cross with the lance of Longinus buried within her chest preventing growth to the lower part of her body.  NERV collect the blood that flows from Lilith's body and use it as LCL, this is picked up on by Shinji who frequently comments on the fact that an Eva's entry plug smells of blood.

Lilith is also the key to the human instrumentality project and the third impact.  Apparently Lilith is capable of instigating the third impact and so is therefore invaluable to both Gendo and SEELE, however, Unit 01 is equally as valuable being built from Lilith, and hence effectively a viable substitute for Lilith should the need arise.
A seven-eyed, bone-white body crucified to a red cross at the heart of NERV. Into this angels side is the Lance of Longinus, a weapon that is able to pearce an angel's AT field. It keeps this angel from regenerating it's legs, which have been ripped off. Also, from Lilith's side, weeps a fluid that is the LCL (Link Connect Fluid) used by NERV in filling the pilot plugs for the Eva pilots.