For me it depends on context - namely, what too modifies/refers to. Here's what I have in mind:
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Scenario 1:
John: Enjoy your meal. (And) have a nice day, too. <-- comma
Scenario 2:
John: Have a nice day.
Fred: (You) have a nice day too. <-- no comma
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Basically, when too is used in the sense of "in addition to (whatever else)", I would put a comma; when it means "me too" (or whoever), I would not put a comma. More examples:
(1)
a. I went to the store. And I stopped at Fred's house, too.
b. I love broccoli. And asparagus, too.
c. We can watch Jaws first, but I definitely want to watch Dracula, too.
In the sentences above, too can be replaced/paraphrased with "in addition", so I'd put a comma.
(2)
a. John stopped at Fred's house, and I did too.
b. You love asparagus? I love asparagus too!
c. Mary's not the only one -- I want to watch Dracula too.
These can be paraphrased with "me too", so I would not put a comma.
I'm not really advocating these usages; they could just be a personal oddity of mine.
What I really think is going on, though, is that there is a difference in prosody (intonation) depending on whether too means "in addition", or rather "me/you/whoever too". Notice that in scenario 1 and sentences (1), where too = "in addition", the sentences up to too have the exact same prosody/intonation pattern regardless of whether too is there or not. This suggests that too is its own prosodic phrase; hence, there is a pause between the main clause and too, and hence why I prefer a comma there.
But in scenario 2 and sentences (2), where too = "me/you/whoever too", the sentences up to too have a different prosody/intonation pattern depending on whether too is there or not. (For example, if you utter sentence (2c) and stop before saying too, it sounds very incomplete; this is not the case with the sentences in (1).) This suggests that, when too is there, it's part of the main clause, hence no pause, hence no comma.