EmailService.php

<?php
namespace My\Package\Service;

use TYPO3\Flow\Annotations as Flow;

/**
 * @Flow\Scope("singleton")
 */
class EmailService {

	/**
	 * @Flow\Inject
	 * @var \TYPO3\Flow\Log\SystemLoggerInterface
	 */
	protected $systemLogger;

	/**
	 * @Flow\Inject
	 * @var \TYPO3\Flow\Configuration\ConfigurationManager
	 */
	protected $configurationManager;

	/**
	 * @Flow\Inject
	 * @var \TYPO3\Flow\Mvc\Routing\RouterInterface
	 */
	protected $router;

	/**
	 * @param string $templateIdentifier name of the email template to use @see renderEmailBody()
	 * @param string $subject subject of the email
	 * @param array $sender sender of the email in the format array('<emailAddress>' => '<name>')
	 * @param array $recipient recipient of the email in the format array('<emailAddress>' => '<name>')
	 * @param array $variables variables that will be available in the email template. in the format array('<key>' => '<value>', ....)
	 * @return boolean TRUE on success, otherwise FALSE
	 */
	public function sendTemplateBasedEmail($templateIdentifier, $subject, array $sender, array $recipient, array $variables = array()) {
		$this->initializeRouter();
		$plaintextBody = $this->renderEmailBody($templateIdentifier, 'txt', $variables);
		$htmlBody = $this->renderEmailBody($templateIdentifier, 'html', $variables);
		$mail = new \TYPO3\SwiftMailer\Message();
		$mail
			->setFrom(array($sender['email'] => $sender['name']))
			->setTo(array($recipient['email'] => $recipient['name']))
			->setSubject($subject)
			->setBody($plaintextBody)
			->addPart($htmlBody, 'text/html');

		return $this->sendMail($mail);
	}

	/**
	 * @param string $templateIdentifier
	 * @param string $format
	 * @param array $variables
	 * @return string
	 */
	protected function renderEmailBody($templateIdentifier, $format, array $variables) {
		$standaloneView = new \TYPO3\Fluid\View\StandaloneView();
		$request = $standaloneView->getRequest();
		$request->setControllerPackageKey('My.Package');
		$templatePathAndFilename = sprintf('resource://My.Package/Private/EmailTemplates/%s.%s', $templateIdentifier, $format);
		$standaloneView->setTemplatePathAndFilename($templatePathAndFilename);
		$standaloneView->assignMultiple($variables);

		return $standaloneView->render();
	}

	/**
	 * Sends a mail and creates a system logger entry if sending failed
	 *
	 * @param \TYPO3\SwiftMailer\Message $mail
	 * @return boolean TRUE on success, otherwise FALSE
	 */
	protected function sendMail(\TYPO3\SwiftMailer\Message $mail) {
		$numberOfRecipients = 0;
			// ignore exceptions but log them
		$exceptionMessage = '';
		try {
			$numberOfRecipients = $mail->send();
		} catch (\Exception $e) {
			$exceptionMessage = $e->getMessage();
		}

		if ($numberOfRecipients < 1) {
			$this->systemLogger->log('Could not sent notification email "' . $mail->getSubject() . '"', LOG_ERR, array(
				'exception' => $exceptionMessage,
				'message' => $mail->getSubject(),
				'id' => (string)$mail->getHeaders()->get('Message-ID')
			));
			return FALSE;
		}
		return TRUE;
	}

	/**
	 * Initialize the injected router-object
	 *
	 * @return void
	 */
	protected function initializeRouter() {
		$routesConfiguration = $this->configurationManager->getConfiguration(\TYPO3\Flow\Configuration\ConfigurationManager::CONFIGURATION_TYPE_ROUTES);
		$this->router->setRoutesConfiguration($routesConfiguration);
	}
}

?>

Usage:

/**
@flow\Inject
@var \My\Package\Service\EmailService / protected $emailService;
*/ ...

$this->emailService->sendTemplateBasedEmail(
'RegistrationConfirmationOutgoing',
'Please confirm registration',
array('admin@example.com' => 'sender'),
array('recipient@example.com' => 'recipient'),
array('variables' => 'available', 'in' => 'template')
);

Note: Initialization of the router (line 101ff) and definition of package key (line 61) is done so that links work in the templates even when invoked from the CLI