What kinds of apps, and what kinds of notifications?
Is it stock apps like Messaging or Gmail, or Third party apps (such as the Phandroid app not notifying of PMs, etc.)?
If Third-party apps, not all of them have the code written in to start a service and check for updates automatically, you have to have initiated the app and have it in memory to poll for updates and so notify you...
If stock apps check under Settings -> Accounts & Sync to see if there are any errors reported for syncing...
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