General Sites
Guide to Neon Genesis Evangelion
Nice design, info on characters and episode synopsis.
Embrace Eva
Not the prettiest page, but includes lots of info including a dictionary and movie synopsis.
Neon Genesis Evangelion Dot Com
A cute design. Tons of well organized links.
Fly Me to the Moon
The official Neon Genesis Evangelion fan listing.

Image Sites
Many rare, high res jpegs.
The MAGI Archives
Used to be an amazing ftp site, but still has lots of rare thumbnails...

Other Sites
Eva Otaku
A page focused on the movies. Includes translations for the Red Cross Book, film screenplay and FAQ.
Shinseiki Evangelion
Includes an excellent translation of the drama track on the third NGE soundtrack. Also has an extremely brief spoiler free synopsis of each tv episode.

Other Anime/Manga
Anime Turnpike
Includes every anime link you can dream of.
An uptodate magazine site that covers Japanese pop culture as well as anime and manga material.
Was an excellent magazine site to keep up with the industry although it hasn't been updated since the webmaster went on hiatus. However, the archives are still well worth visiting. Includes very well written reviews of anime, manga and gaming. Check out their article on NGE.
All you want to know about Miyazaki and his projects.
The Otaku
A resource for numerous anime, including Eva.