I don’t know that I’ve ever really thought about this idiom. It’s very common, and yet it’s really quite a strange one!
Plain meaning: “ought to”
When I say that “you better” do something, I mean that it is what you ought to do. There is a strong expectation that you will do it.
The idiom is used in reference to a verb. In your example, the verb and its object (“think that”) are left off, since it was just stated and doesn’t need to be repeated. So yes, part of the full sentence has been omitted.
Connotation: “or else!”
Very often, it implies that there will be some negative consequence if the expectation is not followed. The speaker might be making a threat, or they might be asserting that a consequence will happen naturally. They might be serious, or be saying it in jest.
What that consequence is may be vague, as it is here. If Phil doesn’t think that Windows stinks and Unix-like OSs are superior, the consequence might be:
- Guido will be disappointed, or feel like his view of the world is shaken.
- Phil gets into trouble with his employer.
- The audience of Linux Journal complains long and loudly.
Other forms and examples
“You better” is a shorter alternative to “you’d better”, which in turn is a contraction of “you had better”. All three are fine, though in my experience, the uncontracted form is much less common.
It doesn’t have to be the second-person pronoun “you”. I can say that “I’d better get some sleep”, or that “Mike better not lose his hat”. The subject can even be left out, in casual use: “It’s late. Better start packing.”
It’s also commonly used with “best” rather than “better”, as in, “You’d best get on with your homework.” There may be a geographic element to which one is more common, but I don’t have any data on that.
While thinking of examples I could cite, for some reason my memory kept bringing up song lyrics that use this idiom. There are quite a lot of them! Here’s a selection from across several decades.
You better not shout, better not cry
You better not pout, I’m telling you why
— Coots & Gillespie (1934), Santa Claus Is Comin’ to Town
You best be believing
I won’t be deceiving my guy
— Mary Wells (1964), My Guy
That’s why I tell you
You’d better be home soon
— Crowded House (1988), Better Be Home Soon
All the other kids with the pumped up kicks
You better run, better run, outrun my gun
— Foster the People (2010), Pumped Up Kicks
Bitch better have my money
Pay me what you owe me
— Rihanna (2015), Bitch Better Have My Money
“Better”, of course, is the comparative of “good” (and “best” is the superlative). I think it’s being used here as an adverb, though, so it’s a form of “well” instead.
So, it seems that the literal meaning is, “You would do (more) well if you chose this action.” But the grammar is still weird. Why “had better [+ infinitive]”? Is it a subjunctive? An imperative? I don’t know!
And why “better” at all? The phrase is used in a context where one alternative is bad. It’s not a case of “this is good, but that is better”.
(On the other hand, the variation between “better” and “best” is easy to understand. If there are only two options, and one is better than the other, then it’s also the best of the two.)
In the end, I think I had better just see it as a fixed idiom, another oddity of English, or else I might be puzzling over it for hours yet.