sorry .. I'm still thinking about it, looking into other themes and so on but I still haven't found the one and only system to keep things in order .. hooks-filters is indeed a cumbersome file.
Let's take a look on all files:
widgets.php - OK .. everything 'bout the Widgets
theme-options.php - OK .. Thematic Options
shortcodes.php - OK .. Shortcodes (currently Footer only, could be more)
scripts.php - OK .. Scripts we need for the menu (more to come?)
page-numbers.php - ?? .. Do we need this one in a separate file?
hooks-filters.php - ?? .. needs to be splitted (new system?)
helpers.php - OK .. everything that goes around the core
dynamic-classes.php - OK .. the markup
discussion.php - OK .. allow discussions in the comments
author-info-avatar.php - ?? .. Do we need this one in a separate file?
What about splitting the hooks-filters according to the markup (still would need a scheme for the file names)?