It depends on whether you have registered with the software provider. I have received genuine software update reminders by email telling me that a new update is out. I usually then go to the website and check what the update provides.
I have always received an email from NVIDIA telling me there is a VISTA update Driver for my desktop , indeed I received one on 29th July this year, but I do know that one is safe, I also get emails from MS saying security updates available and what other security items are happening. But I agree with what JB says I would be quite suspicious of any other emails apart from those two.
I would agree in being suspicious of email notification, unless (as others have said) you registered for some specific software. I guess you could always google to double check if there is an update, or go to the vendor's website & check?
The Java update thing is a bit suspicious, & I've seen on quite a few sites a suspicious notification telling me my Java needs updating when I know full well it doesn't.
Generally I wait for the application to tell me there's an update, and then go from there.