Follow these steps to reset the MySQL root user privileges on Windows:

1- Stop the MySQL service

2- Open a command prompt and run the following command:

D:\MySQL\MySQL Server 4.1\bin>mysqld-nt --skip-grant-tables

3- Open a new command prompt and connect to the mysqld server with this command:

D:\MySQL\MySQL Server 4.1\bin>mysql -u root

4- Issue the following statements in the mysql client:

mysql> FLUSH PRIVILEGES;

mysql> USE mysql;

mysql> REPLACE INTO user VALUES ('localhost','root','','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','','','','',0,0,0,0);

mysql> REPLACE INTO user VALUES ('%','root','','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','Y','','','','',0,0,0,0);

mysql> quit;

5- Open the windows task manager and kill the process with name mysqld-nt.exe

6- Start the MySQL service and now you will have the root privileges back :-)

Note: This article assumes that MySQL was installed on "D:\MySQL\MySQL Server 4.1"