As far as SQLyog is concerned it does not matter. SQLog always uses UTF8 internally no matter how data are stored on the server. Please refer:
http://faq.webyog.com/content/8/148/en/do-i-need-to-set-names-to-display-characters-of-my-language.html.
Besides this is not the best place for asking web application design questions. You are welcome to do so, but it is unlikely that you will meet experts in that matter here. However we at Webyog have been using UTF8 for all our web for more than 5 years now (and that is unrelated to HTML5) .