Android is still evolving, but there was a definite design decision to allow individual apps to manage their own notifications, though of course there is a centralized set of controls for core functions - phone especially. I also think that there is some reluctance to allow one app to control the settings of another - for security purposes, Android was designed to prevent apps from stepping on other apps.
Now, there is a way that you could manage this if you use Setting Profiles Full, if you are willing to make some small compromises, and you are using the Gmail app for email, rather than the Messaging app. (Actually, it could be that the messaging app would be affected as well.... I use only the Gmail app for mail myself.)
SP Full allows you to turn off background sync, which would turn off the Gmail app syncing (and, obviously, stop those notifications.) However, at least some Twitter apps do not turn off syncing if you turn off autosync, so they would still get notifications. I'm not sure about Yahoo Messenger, but I would guess that it is the same.
SP Full does allow you to create a profile that changes the default notification sound to silent. If you set the Messaging app to use the default notification sound, this would still make the Messaging app get notifications, but they would not make a noise. As long as your Twitter app and Yahoo Messenger were set to use a different sound for notifications, they should continue to make use those sounds, however.
So, in SP Full, you'd create a couple of profiles. One (we'll call it sound off) will set the Notification ringtone to "silent", turn Vibrate for notifications off, and set Autosync off. Sound on would change the Notification rington to whatever you use normally, turn on vibrate for notifications if you want that, and turn autosync back on.
Then you could create a couple of Rules, that are time based, which activate each of those Profiles at specific times.
So, I take it back - you could use SP Full, so long as you had different notification ringtones from the default for Yahoo Messenger and your Twitter app.
After typing all of this, I am assuming that when you want to stop notifications for specific apps, you are talking about sounds, rather than just discretely stopping the app from running in the background.
