...
If you're looking for the
literal descriptive sense, Theseus, there's
μακρυλαίμης / μακρολαίμης or
λέλεκας / λελέκι.
Though the latter is generally used for anyone tall and gangly, it does convey the picture of someone with a long neck, resembling the stork where it comes from.
If you're looking for the sense of
geek (I believe that in the US it's common as "pencil-neck geek", a catchphrase Wikipedia says was coined by a "wrestler",
Fred Blassie;
it comes with a song, too! 
), you'll find plenty of suggestions like
σπασίκλας, φυτό, φύτουκλας in the thread for
nerd, geek, dork, or even
γκικ in the thread for the slang of the young.
For the 3rd sense Urban Dictionary mentions (
One who works in an office doing a hum-drum type job. Typical examples: Anyone who works in IT, accountants and people in supply departments.), I guess
χαρτογιακάς, γραφιάς or
υπαλληλάκος would be close in meaning
(and demeaning).
I'll leave the sense of spineless, weak and timid for the next posters; nothing comes to mind right now with that kind of colloquial flavour - just the mild
δειλός,
άτολμος or
συνεσταλμένος - except maybe
ανθρωπάκι.
