Finally I did it like this:
RewriteEngine on
RewriteBase /
########## SITE 1
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^site1/(.*)$ site1/index.php?url=$1 [L, QSA]
########## SITE 2
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^site2/(.*)$ site2/index.php?url=$1 [L, QSA]
########## SITE 3 (by URL)
RewriteCond %{HTTP_HOST} ^mysite3.com$ [OR]
RewriteCond %{HTTP_HOST} ^www.mysite3.com$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?url=$1 [L, QSA]