.NET 4 is required to run the theme manager; You can download it here
Colors are defined in Settings ‣ Preferences ‣ Colors. Text Colors set the palette for events to use. The rest like background color directly affect parts of the UI.
mIRC colors (0-15) are what you refer to when sending colored text over IRC for others to see and vice versa, because of this they should somewhat follow a set of standards so clients can agree 4 is red.
Local colors (16-31) are to be used by HexChat only and can be anything you wish, these are typically what you use in your events.
Text events control the look of every event you see. They can be customized in Settings ‣ Text Events using these codes to format it:
Always hit enter after editing a field.
HexChat comes with built in icons for the tray, user list, and channel tree (which can be disabled in Preferences). You can use custom icons by placing icons (16x16 recommended) in an icons subdir, which may need to be created, within your config folder. The icons must be named as follows:
To customize more than just text color you can place a gtkrc file in <installdir>\etc\gtk-2.0