Команда
\usepackage[english,greek]{babel}
заставляет MikTeX 2.9 работать вечно.
ОС Windows 7
Выходной сигнал:
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (MiKTeX 2.9)
entering extended mode
(C:/Users/x/AppData/Local/Temp/lyx_tmpdir.Hp3100/lyx_tmpbuf2/negreponti-1.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, afrikaans, ancientgreek, ar
abic, armenian, assamese, basque, bengali, bokmal, bulgarian, catalan, coptic,
croatian, czech, danish, dutch, esperanto, estonian, farsi, finnish, french, ga
lician, german, greek, gujarati, hindi, hungarian, icelandic, indonesian, inter
lingua, irish, italian, kannada, kurmanji, latin, latvian, lithuanian, malayala
m, marathi, mongolian, mongolianlmc, monogreek, ngerman, nynorsk, oriya, panjab
i, pinyin, polish, portuguese, romanian, russian, sanskrit, serbian, slovak, sl
ovenian, spanish, swedish, swissgerman, tamil, telugu, turkish, turkmen, ukengl
ish, ukrainian, uppersorbian, usenglishmax, welsh, loaded.
Отредактировано:из комментария ОП, небольшой код:
\makeatletter \makeatother
\documentclass[11pt,oneside]{amsart}
\usepackage[iso-8859-7]{inputenc}
\usepackage[a4paper]{geometry}
\usepackage{amsthm}
\usepackage{amstext}
\usepackage{amssymb}
\makeatletter
\usepackage[english,greek]{babel}
%\usepackage[default]{gfsneohellenic}
%\usepackage[LGR,T1]{fontenc} %% LGR encoding is needed for gfsneohellenic
\makeatother
\begin{document} klkk \greektext γφγγ
\end{document}