In no particular order
ICON (post GWIII) and Zenith: started out strong but collapsed due to failure to create internal community. They also mooched off of whoever was in power and had no opinions of their own.
WTF: Gigantic but does very little and when they show their faces here, it's really disappointing.
Heroes of the Union: Nice people but completely incompetent. They got themselves attacked pretty much by incompetence. I don't even remember what they did at the time (i think it was accidentally admitting a ZIed person because they didn't investigate members)but I remember going "How can you be so stupid?"
Order of Feudalistic Security: Gonzoczar's post GATO alliance. At one point, they had a "treaty us or be attacked" policy.
Andromeda: Hard to think of a better connected but worthless alliance. Ephraim Gray was a treaty whore extraordinaire and loved making promises he couldn't actually keep due to his alliance's size.
Honorable mention for SOS Brigade and any other alliance that ever used anime as a theme because pedophilia and beastiality are not cool.