http://wordpress.org/extend/themes/ : The official Wordpress.org themes section. Features search by number of columns, primary colour of the theme, theme topic, fixed or flexible width and some of the features like custom-colours, theme options, translation ready, buddypress and so on. Features most of the themes but misses out on some of the great free themes offered by commercial Wordpress theme developers. No information about the version of Wordpress the theme is developed for.

http://topwpthemes.com/ :  Features themes by category, number of columns, left or right sidebar and if widget ready or not. No search option. Great collection of themes.

http://wordpressthemesbase.com/ : Features themes by categories and features. Offers search feature and also top downloaded, rated and viewed.

http://www.themes2wp.com/ : Free and Premium themes. Found some very neat themes on this site. Check it out.

http://www.wpthemes360.com/ : Just thumbnails of many many themes. No search or any other feature.

and more other directories coming soon…

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