The encoding is stored in the header of the file itself. Notepad++ and similar programs usually provide a number of options to change and view it.
Additionally, you can provide a value by using the meta tag:
<meta charset="UTF-8">
(HTML5)
<meta http-equiv="Content-Type" content="text/html;charset=utf-8">
(HTML4)
Those tags are used by browsers to parse your file. However, they do not define the encoding of the file itself (and that's what seems to be happening in your case: your file has encoding A, and the browser is trying to read encoding B), and browsers can ignore those conditions.
The default encoding can also be defined (and overwritten) by your server. A sample .htaccess encoding configuration:
AddDefaultCharset utf-8
AddType 'text/html; charset=utf-8' .html .htm .shtml
UTF-8 is the recommended encoding standard for the web.