Perhaps the greatest feature of Horde and all of it's modules is the flexibility to adapt to a myriad of different uses and I would expect that eventually, a more integrated system of managing 'defaults' will become part of the code but at this moment in time, the only way to effect settings system wide is to edit the various prefs.php file inside each module.
In general: Add any local changes to a prefs.local.php or a prefs.d/<name>,php file. Never change prefs.php because this file is overwritten on upgrade and contains vital system information about the preferences that must match the other parts of the system. For instance,
kronolith/config/prefs.php contains:
// Address book(s) to use when expanding addresses ``
// Refer to turba/config/sources.php for possible source values
//
// You can provide default values this way:
// 'value' => json_encode(array('source_one', 'source_two'))
$_prefs['search_sources'] = array(
'value' => ''
);
To change the default value add the following PHP code to either kronolith/config/prefs.local.php or kronolith/config/prefs.d/name.php name can be any name you like, I prefer the local hostname:
<?PHP $_prefs['search_sources']['value'] = '["favourites"]';