The store-windows-on-suspend behavior is normally controlled in System Preferences > General Settings using the Restore windows when quitting and re-opening apps preference.
This pref translates into a global preference called NSQuitAlwaysKeepsWindows. When enabled, Lion attempts to restore windows to their previous positions and their most recent contents. The preference is stored into .GlobalPreferences.plist. (Notice that first period? It makes it invisible.)
What's interesting is that Lion does respect this preference on a per-app basis even though there's no such functionality built into preferences or into apps. The NSQuitAlwaysKeepsWindows preference can be used in application user defaults files, which are found in your home Library/Preferences folder.
Auntie put together an application (the "Resuminator"; windows won't be back) to help you with this, which you can download here. When run, you can select an application and override resume for just that application.
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