This plug-in is complimented well by P3 Plugin Profiler. Alas, that plug-in reveals that Organizer adds about 118.1 milliseconds of overhead on my site, however I was able to shed 84 milliseconds and a few queries by selectively disabling just 3 plug-ins (which P3 claimed as 64.9 milliseconds) for all pages but the 3 that use their provided short-codes.
Although I'm not sure what the point of being able to reorder plug-in execution is, I especially like that Organizer moves the disabled plug-ins to the bottom of the the listing of All plug-ins.
I was also glad to see that the author made sure to allow for "disabled" plug-ins to remain accessible in the admin area. Although it is not clear form the plug-in description, selective plug-in enabling applies to posts as well as plug-ins :-) Although this might not be terribly common, I have one or two that provide shortcodes which are only used in particular places.
Now for the nits:
I would much prefer that the plugin settings 1) be added to the plug-ins menu--a more natural place for them--and not created as its own top-level menu 2) also be linked to from the plug-in entry.
I would like to disable a number of plug-ins that affect the administration interface only, and enable them for wp-admin only. A simple interface option to do so might be nice, but this should also be possible with the Arbitrary URL system. Unfortunately, the Arbitrary URLs interface is not intuitive. It seems as though the labels for the lists of plug-ins are swapped. More problematic is that the plug-in will not accept a relative URL. Many sites can be accessed with or without www and with or without SSL, relative URls are also shorter to type and should be be the preferred entry form.