html then sql
For software it depends both on the function of the software and the target environment. Nothing general can be said about it. Your iPhone app will use a different programming language than your Windows utility.
The best tool to make websites depends on the functionality the website needs. There's nothing wrong with using a CMS like joomla or wordpress for certain websites, like there's nothing wrong with using .Net or Java EE or PHP for other types of websites or simple html for still others.
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