Just for information's sake, the list, as it appears in the first 

animation,  

 is as follows.
 

I probably should have said this earlier, both Rod and John have stated that 
the list is no longer ENTIRELY valid as pertains to order; also, if you watch 
it realllllyyyyy carefully when the GIFs shift, you can see that the names 
change around a tad.

 >  Also, I don't see Daoloth as a particularly good choice (see below).  
Other 

 options might be Glaaki, Nyogtha, or Zoth-Ommog.

Someone brought up Glaaki back when people were trying to guess who the guy 
swiming to Toronto would be. To quote John, "Glaki? Glaaki is silly. There 
will be NO Glaaki in this story."
  

 Cthugha'll be difficult.  As a being composed entirely of plasma, with no 
 solid mass, the Eva will be unable to touch this GOO nor can physical 
 attacks hurt it.  

Meh. It never stopped them before; in the anime Leliel, Iruel, and Armisael 
can't be harmed by conventional means, but they beat THEM.  

 Hey, are the Eva's going to travel to the GOOs, like they did with 

Ithaqua?  

They would almost have to. Most of these guys aren't exactly the moblest 
beings in creation; they can cross the light-years at FTL speeds, but once 
they get here they seem to be utterly incapable of moving around. 
 

 Because, as you may know, some of these Great Old Ones aren't found near 
 Japan.  Yig and Tsathoggua are buried under North America in K'n-Yan and 
 N'kai.  Yig's tomb in K'n-Yan is supposed to be under Oklahoma.  

Y'golonac's 

Actually, I beleive Oklahoma is where they initially found Atlach-Nacha. 
Remember the very first scene in COAEG 1, the part with the gratuitous Mythos 
author cameos?

Plus keep in mind that SOMETHING has to be down in LCL Plant Main Line Number 
Three, strapped to an Elder Sign, giving up the LCL.

Unless they're using Shoggoths or Ubbo-Sathla....
 

 Lastly (in this section at least), while Cthulhu is really cool and all, I 
 think that you really ought to place him before Nyarlathotep.  While he's 
 got a lot of name recognition, his power level much less than 
 Nyarlathotep's.  The biggest threat should come last.

Noooottttttt neccessarily....... 'Tep will be in his human form, remember; 
when he's human, Nyarlathotep's power is scaled wayyyyyyyyyy back, almost all 
the way to normal human levels. His only exceptional attribute then is his 
magic, and considering the books they've read, Fuyutsuki, Gendo, and Ritsuko 
would have no trouble countering him. Not that it'll likely come to that, 
but.......
  

 >And yes, Nyarlatotep is on the elist (the ONLY Outer God on the >list) 

and 

 >as for him standing in for Kaoru, that's one of the >biggest no-brainers 
 >around.
 
 Actually, Daoloth is also an Outer God.  Although I really wonder why 
 Daoloth would even bother turning up.  Only people who take drug that 

shift 

 them into phase with higher dimensions are ever bothered by Daoloth, or 
 occasionally folks who muck about with funny-looking sculptures.  And how 
 would Evas be any use against something that effectively IS a higher 
 dimension, and like Yog-Sothoth or Azathoth is probably a fundamental part 
 of reality?

Actually, I fully believe that Yoggie made a cameo in the original series. 
Remeber Leliel, the 12th Angel? Big, black void, gateway to another universe, 
sucks half the city in, pocket diemnsion?
 
Think about it.

-Mercutio
"A plague 'a both your houses!"