No, there are no credible studies that prove this, and there doesn't have to be studies to disprove this (nor are there likely to be).
In brief, there has been no attempt to offer any sort of mechanism (within the scientific realm) by which a persons thoughts or intentions could modify water, or rot rice, or have any other kind of effect. On the other hand, there are a great many ways to explain why so many anecdotes appear all over the internet that support the theory. Confirmation bias and general disregard for the scientific method are probably the biggest contributors.
The lack of counterclaims is understandable. The claim is so absurd that only non-scientific minds would waste their time attempting to reproduce the result. Few respectable scientists would waste their time or money arranging:
- A few hundred jars of rice (for statistical significance),
- A blind party to divide jars into three groups: positive and negative intentions, as well as a group which will not be interacted with (a control group),
- Controls for extremely influential variables such as temperature and humidity (controlled variables),
- Another blind party of "believers" interacting with the jars each day with their genuine intentions of affecting the rice with their thoughts (double blind),
- Yet another blind party evaluate the amount of rot on each jar with no knowledge of how jars were treated or what group they were part of (triple blind study).
As you can see, there's little more than common sense required to come up with even a mildly scientific method - but lots of effort in performing a rigorous experiment. (Arguably the most taxing requirement being the gathering of "believers".)
Because all anecdotal experiments such as youtube videos and blogs, as well as Masaru Emoto and his followers' own experiments do not address all of the above considerations (most address none of them), they cannot be considered credible.
Jokes aside, it's generally not considered the responsibility of the scientific community to disprove every stray bit of pseudoscience that attains a certain amount of popularity. For that reason, there will most likely never be studies with the goal of disproving them. It would be a different case if Masaru Emoto had ever submitted a publication for peer review to the scientific community, but his only uncoverable peer reviewed publication (on intentions affecting the formation of water crystals) was to the Journal of
Alternative and Complementary Medicine. That alone should tell you how much weight is placed in his theories. Furthermore, a one million dollar prize was offered to anyone who could reproduce his results in a double blind study, which has never been claimed. 
So in conclusion, there's likely no credible studies that prove this theory, because none of the experiments claiming to provide supporting evidence for theory are scientifically rigorous (including the experiment described in the question). There's no credible studies disproving this theory because there is no incentive or requirement in the scientific community to address this pseudoscience. There's also no reason for anyone to believe that such a phenomenon is possible if they take the time to research the proposed mechanism for the power of thought and how it fails to measure up to common scientific knowledge.