You can use a 301 redirect in your htaccess which is the most appropriate to denote that something has moved (mostly search engine wise).
Just put a line like this in the drupal .htaccess or even create a separate .htaccess in the folder you user (if you still have it)
redirect 301 /your_folder http://www.yourdomain.com/
What I usually do with drupal is have it in a subfolder and when I am ready to move it to the main domain I just create an .htaccess file in the root directory with rewriting and never move the actual files. I have found that this is more convenient especially when wanting to change the main domain content fast (say restore from a backup, without messing with existing files, create a new dir and change .htaccess to point to that).
my .htaccess looks like:
Options -Indexes
Options +FollowSymLinks
RewriteEngine on
# Redirect all user to WWW
RewriteCond %{HTTP_HOST} !^www\.
RewriteRule ^(.*)$ http://www.%{HTTP_HOST}/$1 [R=301,L]
# Serve Drupal 7 from sub directory in web root
RewriteRule ^$ my_folder/index.php [L]
RewriteCond %{DOCUMENT_ROOT}/my_folder%{REQUEST_URI} -f
RewriteRule .* my_folder/$0 [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* my_folder/index.php?q=$0 [QSA]