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For users logged in with frontEndUsers module.

What is the best way to get the currently logged in user id?

well if you want it in smarty use the customcontent module

if you want it in a udt, you can get a reference to the FrontEndUsers module and use the functions in FrontEndUsers.api.php

This is from within a module in php.

$feu =& $this->GetModuleInstance('FrontEndUsers');
$uid = $feu->LoggedInId();