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I already have a backup of my system on Time Machine, but will it restore my application preferences too when I migrate to a new system? Even if it is Lion? (I come from Snow Leopard) And what about those apps that have their data in Library>Application Support?

Do I have to manually copy and restore .plist files or is there a Backup app smart enough to copy them together with the .app file?

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Your preferences will be copied if you allow Migration Assistant to copy your data from a Time Machine backup (one of the options at the beginning of the installation).

Time Machine backs up just about everything except Mac OS X and other system resource files. So, your preferences will be saved.

I've tested this migrating from 10.6 to 10.6, and I've migrated from another Mac directly from 10.6 to 10.7. That process is, in practice, the same.
So, your preferences will be copied from your Time Machine backup to your new system.

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Great answer - do be aware that the convention is to upgrade preferences on first launch (and Migration Assistant will tweak system level and known preferences to prepare for Lion) - this isn't a backwards friendly process so you often can't go back once the migration has happened. Keep the old 10.6 backups if you ever want to go back. –  bmike Jul 15 '11 at 14:53
    
Thanks for your answer...but I still have some doubts. TM backs up everything, but doesn't necessarily restores everything too! What if I decide to restore just iTunes library, iPhoto and a couple of apps? Is it smart enough to restore prefs too (I mean, just those I need)? I certainly won't restore my whole account folder after installing Lion... –  andrew_bomb Jul 15 '11 at 15:34
    
If you choose to restore just specific apps, you won't be able to use Migration Assistant. You'll have to copy everything manually. So, you'll have to copy the app, its resources, and its preferences manually. –  Nathan Greenstein Jul 15 '11 at 23:55
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