Which files in the “MySQL-5.0.27-win32” folder do i need to backup?
You are using a very old, end-of-life, and unsupported version of MySQL.

There is not exactly a correct answer to your question, because it is impossible in many cases to safely back up or clone a MySQL server that is still running.

The only absolutely safe way to copy data using this method is by stopping the mysqld process, gracefully, and copying all of the files, for all of the databases.

If you are using MyISAM, which, again, you almost certainly should not, it is possible to copy a single database by copying all of the files in that database's named directory, but the tables have to be locked and flushed, or the backup will either not contain the most recent changes, or will be corrupt.

If you are using InnoDB, it is almost impossible to copy only one database from one server by copying files, unless you use the "transportable tablespaces" feature introduced in MySQL 5.6.

The correct answer to the question is "don't do it this way."

The correct solution is to use mysqldump to make the backup, which does not copy files at all.  Instead, it creates a file containing the SQL statements necessary to recreate your tables and reinsert the data that was in those tables when the backup was made.

The output of mysqldump is also human-readable, so you can actually examine what's in the backup.

http://dev.mysql.com/doc/refman/5.0/en/mysqldump.html