RewriteRule ^wiki/?(.*)$ /w/index.php?title=$1 [L,QSA]
So I suggest you try changing that line to the correct conditions for your site.
So to change http://www.mysite.com/index.php?title=Article to http://www.mysite.com/index.php/title=Article or better http://www.mysite.com/Article what I have to write in .htaccess? Excuse me but I don't know how to use rewrite.
Many thanks,
Giovanni