why do certain applications open automatically

Which ones do you mean and what version of the OS are you using?

With Lion, all of your apps and windows open up o the spot where you were when you last shut down your Mac.

To add to this, if the OP is referring to applications automatically opening upon logging in, then that can be disabled from System Preferences --> User Accounts --> Login Items

If you're using Lion, and the apps open automatically when you start up/log in, it's down to one of two things. Either

a) you had the application open when you shut down last time, or

b) you have that application set to open automatically.

If you don't want (a) happening, either quit the application completely before you shut down, or turn off all app resuming through System Preferences - General - untick "Restore windows when quitting and re-opening apps".

If the apps re-open even if you quit them before shutting down, check System Preferences - Accounts - Login Items. Delete any programs from the list that you don't want auto-launching when you log in.

Matt

Two different reasons.

They could be in your login items in System Preferences > Users & Groups > Login Items tab

or when you restarted or shutdown, you didn't uncheck this option:

Regards,

Captfred