Plugins (Tools > Add-ons > Plugins) like the Adobe Flash player and the Java plugin are not affected by updating and should still be working. Extensions (Tools > Add-ons > Extensions) like the Java Console extension have a minimum and maximum version and may get disabled.
Extensions are provided by third-party developers and it may take some time to have them updated or the creator may decide to stop the support for the new Firefox version and abandon the extension like happened with the Google Toolbar.

Thank you Cor-el. I made the download of version 7 and Zynga tool bar as other javas are not compatible so I will have to uninstall also this version and will be back to the old version 4.

Firefox 7 is a Beta version right now, 5 weeks away form being released. If an add-on isn't compatible with Firefox 6, it isn't going to be compatible with a pre-release version such as a Beta.

Thank you the-edmeister. These problems began with version 6 so Mozilla should have fixed these issues. If all the previous versions were compatible with these adds-on - a lot of them - why make new versions that are not.... sorry but I do not understand as several other browsers does not have them. I will stay with version 5 that is working well until Mozilla release a version compatible with all the adds-on.