I believe the new Icon Packager version 3 will be capable of changing even more icons than version 2.5 can currently change.
Version 3 is in the works and should be out as soon as the final bugs are worked out.
As for your Cryo64 package, that pack is not as comprehensive as some available (i.e., Utopia pack by Mormegil).
The more icons (especially file type icons) that are made for the pack, the greater the number of system and file type icons can be changed by Icon Packager.
To the best of my knowledge, the current limitations in the full version of Icon Packager 2.5 are some of the control panel icons, a couple icons in the taskpane of say "Save as" dialog, and of course Program Icons - which are supplied by the company who wrote those programs.
You can change some of those program icons individually if you wish, by going to "C:\Documents and Settings\All Users\Start Menu\Programs" folder (where "C" is the letter drive > right-click on the program icon > select Properties > Shortcut tab > Change Icon.. button > Browse to ".ico" image > select and Apply.
For some programs, the "Change Icon..." button may be greyed out - in this case, if you still want to change the program icon, you would need to create a new shortcut in the "C:\Documents and Settings\All Users\Start Menu\Programs" folder which allows you to change the icon image. Note - this will give you a modified icon and the original default icon in the menu.
If you remove the default program icon (which you would want to do if you want the modified one associated with the program), you will want to save the default icon to a backup folder, or use the program install disc to restore the default "Start Menu > All Programs" icon for the relevant program.
I hope this answers some of your questions.