System.out.println(new String(alias.getBytes("UTF-8"), "Windows-1251")); // теперь "îò"

import java.security.KeyStore;
import java.util.Enumeration;

public class TestEncoding {
    public static void main(String[] args) throws Exception{
        KeyStore ks = KeyStore.getInstance("Windows-MY");
        ks.load(null, null);
        Enumeration<String> aliases = ks.aliases();
        
        while (aliases.hasMoreElements()) {
            String alias = aliases.nextElement();
            System.out.println("alias: " + alias);
        }
    }
}

        String text = "îò";
        Set<String> keySet = Charset.availableCharsets().keySet();
        for (String key : keySet) {
            System.out.println("From UTF-8 to " + key + ": " + new String(text.getBytes("UTF-8"), key));
        }