It is currently only possible to assign modules to menu items in one of three ways:
ALL - the module will show on all page views.
NONE - the module will show on no page views.
SELECT- the module will show on the selected page views.
It is not currently possible to assign modules to menu items in a selective/exclusive manner, i.e. a module cannot be set to "show on ALL page views EXCEPTthose specified".
2. Problem-
Because modules cannot be assigned in an exclusive manner, it becomes difficult to manage the layout of complex wesites.
Eg. A site may contain two page views- Home & Page View 1- and two articles- Article 1 & Article 2. The site contains two menu items- Home which is a Front Page Blog Layout and Link 2 which is an Article Layout to Article 1. Several modules are published on the site. Module 1 is assigned to ALL Menu Items. Module 2 is assigned to NONE. Module 3 is assigned only to the Home Menu Item. Module 4 must show on all site page views except Home and so is assigned to Link 2.
Module 1, Module 2 and Module 3 function as needed for proper site structure. Module 1 shows on all page views. Module 2 never shows on any page views. Module 3 only shows on the Home page view. At first glance, Module 4 also seems to function correctly. When a user selects Article 1, they see Module 4. This occurs regardless of whether the user selects Article 1 by clicking the Link 2 Menu Item or the linkable title to Article 1 or a 'Read more' link on Article 1. However, the site structure calls for Module 4 to appear on all page views except Home. Therefore, when a user selects the linkable title of Article 2 or a 'Read more' link on Article 2, Module 4 fails to appear on the resulting page view.
I do not believe this is a bug but rather a failure to include complete logic in Menu Item assignment.
3. Current workaround-
The only current workaround to this issue is to create a Menu Item for each Article on a site and specifically assign the appropriate Modules to those Menu Items. To keep the Menu on the site from growing too large, these Menu Items can be placed in a separate Menu which can be left unpublished. The Menu Items, however, must be published to the Menu.
On very large sites or sites with frequent Article creations, this workaround quickly becomes unwieldy.
4. What is needed-
To complete the logic, Menu Item assignment should include the following 4 possible scenarios:
ALL - works on all page views. (Positive inclusive logic)
NONE - works on all page views. (Negative inclusive logic)
SELECT (or ACCEPT)- works on selected page views. (Positive exclusive logic)
These are available, but this is missing:
EXCEPT- works on selected page views. (Negative exclusive logic)
5. Implementation-
5.1 Code changes-
5.1a Current code-
to be added
5.1b Additional code-
to be added
5.2 User Interface changes-
Here is what we have:

And here is what we need:

6. Compatability-
This fix should pose no issues with backward compatability since it does not affect the current logic implemented in the application. It only presents an additional logical level. Previously configured Menus, Menu Items and Modules would still function as they have been configured. The administrator would simply have the added ability to exclude modules from specific pages.
7. References-
http://forum.joomla.org/viewtopic.php?f=428&p=1203860