I have a greek site with greek domain (gr) and even so, the keyword list of google shows in the first places the greek equivalent words of the common words like "in", "a", "and",etc. All them would be greek's Stop Words Thanks for any help
My Greek site has similar data. My top keywords under "Optimization" -> "Content Keywords" are το, για, and της, the Greek words for it, for, and of.
I've spot checked my site in several other languages. Spanish, Italian, and Arabic don't appear to exhibit this behavior.
This appears to be a bug in Google Webmaster Tools. It appears that for Greek sites, they are not properly identifying important words compared to common words. Since this issue affects multiple Greek sites, I wouldn't worry to much about it. Google should be able to fix it at some point. In Webmaster Tools you could tell Google about this problem using "Help" -> "Send Feedback".