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What effect does a good research paper have on a university's worldwide rankings?

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None. One good paper makes its author(s) look good, but does not make the university more or less remarkable (either in term of perception by the research community or rankings). It takes a lot of good output (papers, conferences, etc.) for people to start saying “hey, that university has great research done in so many research groups, it looks like a great place”, and for whatever rankings to be affected.

Unless by “good” you mean “outstanding”, not in the academic sense “quite okay but I’m writing in hyperbolic style” but in the meaning of “exceptionally good; clearly noticeable”. One groundbreaking (Nobel level, if you wish) discovery made at a single institution will help it.

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    One groundbreaking (Nobel level, if you wish) discovery made at a single institution will help it. — [citation needed]
    – JeffE
    Commented Apr 3, 2013 at 8:41
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    @JeffE if the University of X creates, say, an AIDS vaccine that is talked about in the media, it creates a lot of good (national and international) publicity for it. I have a few examples in France of universities whose funding dramatically improved after they received the spotlight (I'm thinking about Pierre Gilles de Gennes and Jean-Marie Lehn's institutions, for example)
    – F'x
    Commented Apr 3, 2013 at 10:03
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A single good research paper typically has a very small impact on the university's ranking and prestige. However, universities are very large organisations. Any one university may be producing thousands of publications each year. Thus, the presence or absence of one publication is unlikely to change the ranking of a university on some prestige or publication based league table.

That said, each publication (and especially the "good" ones) does play its role in the overall evaluation of prestige. Thus, if a single good publication contributed .01% or .1% of the total citations (or other prestige generating effects) that a university received in a given period, then that is still important. I remember hearing that a study that received a lot of publicity was supposed to have generated $200,000 in free advertising exposure for the university. Presumably similar quantifications could be applied to university prestige. While the contribution of one publication relative to the prestige of an entire university is small, the absolute value may still be substantial.

Furthermore the influence of one good publication on prestige naturally amplifies as you go to smaller groupings from nation to university to faculty to department to research group to individual researcher.

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