The Times Educational Supplement list for 2006 http://www.ui.edu/indonesia/extra/tabelqs.pdf lists four Turkish universities highest rated one is Istanbul Technical University at 349th in the world, then Istanbul University at 358, Bilkent at 401, Sabanci at 454.

I think its also good to mention what this actually means:

Universities were placed in the table with the help of findings from a survey for the THES of 1,300 academics in 88 countries. They were asked to name the best institutions in the fields that they felt knowledgeable about.
The table also included data on the amount of cited research produced by faculty members as an indicator of intellectual vitality, the ratio of faculty to student numbers and a university's success in attracting foreign students and internationally renowned academics in the global market for education. The five factors were weighted and transformed against a scale that gave the top university 1,000 points and ranked everyone else as a proportion of that score.Harvard, whose faculty members have won 40 Nobel prizes, emerged as the world's best university by a considerable distance, with second-placed Berkeley rated 120 points behind at 880.2. Oxford scored 731.8, slightly ahead of Cambridge on 725.4.