Hooks for alt_doc.php:
$TYPO3_CONF_VARS['SC_OPTIONS']['cms']['recordAccess'] (the same is also for tm_contentaccess).
$TYPO3_CONF_VARS['SC_OPTIONS']['cms']['addAlt_docTopLinks']
$TYPO3_CONF_VARS['SC_OPTIONS']['recordAccess']['addAlt_docBottomLinks']
Hook for resetting setting module list:
$TYPO3_CONF_VARS['SC_OPTIONS']['class.t3lib_loadmodules.php']['moduleConfiguration']
Look at the source code of 'class.tx_tmsharedlib_moduleconfiguration.php'.
Added also hooks for User > Setup:
$TYPO3_CONF_VARS['EXTCONF']['setup']['extraItems_1']
$TYPO3_CONF_VARS['EXTCONF']['setup']['extraItems_2']
$TYPO3_CONF_VARS['EXTCONF']['setup']['storeIncomingData']
First two just adds new items and functions should return a string. Concerning the latter function should make a reference to original variables. Use function like 'function storeIncomingData(&$BE_USER, &$d)'.
$TYPO3_CONF_VARS['EXTCONF'][TM_SHARED_LIB_EXTkey]['addSharedTopLinks']
That is for adding some new items for additional tabbed menu.
For backend modules hook for function 'viewPageIcon' (that function relates with 'template.php'):
$TYPO3_CONF_VARS['SC_OPTIONS']['typo3/template.php']['addViewPageIcons']
