We can assign the custom email template for mailing in magento. For this we have template tag in xml file. Here I am assigning new email template for requesting quote in contact us form. Below are the steps you can perform to assign custom email template -

1) Write following lines in config.xml of your module -

<template>
            <email>
                <quote_mail module="module_name">
                    <label>Quote Requested</label>
                    <file>quote_request.html</file>  
                    <type>html</type>
                </quote_mail>
            </email>
</template>

2) Now create a html file in your language locale folder e.g. in app/locale/en_US/template/email/ folder create quote_request.html file with the variables you want to use in html file to display info.

3) Now create the function in the controller to send email and assign a value to the variables to pass in html file.

public function sendCustomMail()
{
    /** content of the mail **/
    $mail          =   new Zend_Mail();
    $mailFrom      =   "sender@email.com";
    $receiverName      =   'donotreply';
    $mailTo            =   'example@example.com';
    $subjectName       =   'Subject of mail';

    /** email variables **/
    $emailTemplateVariables        = array();  
    $emailTemplateVariables['firstName']   = "firstname";
    $emailTemplateVariables['lastName']    = "lastname";
    $emailTemplateVariables['emailAddress'] = "request@email.com";
    $emailTemplateVariables['telephone']   = "number of mobile of receiver";

    /** load custom email template which we have created to send mail **/
    $emailTemplate     = Mage::getModel('core/email_template')->loadDefault('quote_mail');  // where quote_mail is our template tag which decide which file to be loaded for the mail //

    $emailTemplate->setSenderName(Mage::helper('core')->escapeHtml($emailTemplateVariables['firstName'])." ".Mage::helper('core')->escapeHtml($emailTemplateVariables['lastName']));
    $emailTemplate->setSenderEmail($emailTemplateVariables['emailAddress']);
    $emailTemplate->setType('html');
    $emailTemplate->setTemplateSubject($subjectName);
    $emailTemplate->send($mailTo, $receiverName, $emailTemplateVariables);
    Mage::getSingleton('customer/session')->addSuccess($this->__('Mail has been sent successfully.'));
    Mage::app()->getFrontController()->getResponse()->setRedirect(Mage::getBaseUrl());
    /** End **/
}

4) Now to use these variables in a html file you have to call using {{var firstName}} , this will show the value of 'firstName' variable. Similary you can use rest of the variables as per requirement in a template file.

By this you can call create and call any custom html file for mailing if you don't want to use the default mailing files.