I don't know enough about cold fusion, so I haven't read that part. As for relativity theory, it seems that the only valid argument against it presented in the linked article is, translated into more "lesswrongian" language, that doubting special relativity strongly endangers your status. Which is true, at least in general. Then they mention a "Modified Lorentz Aether Theory" without giving a single link to a place where this theory is explained, and support it by saying that the Michelson-Morley experiment conducted in 1887 in fact gave slightly different results than it is now believed it gave - as if these results were not anyway screened off by more recent experiments of the same kind.

The overall feeling I got from reading the passages is that the physical community is ready to censor any theory which doesn't precisely agree with special relativity. Which is a nonsense. First of all, general relativity itself extends special relativity and thus disagrees with it, and the differences between GR and SR are arguably bigger than between SR and Newton. Moreover, practically all physicists expect GR to break somewhere, at Planck scale at the latest.

Well, nobody really believes that the progress will take us back to æther. There is nothing strange with that. The authors of Suppressed Science have, as usual in similar debates, written about how the Newtonian physics was supposed to be absolutely correct until it turned out to be false, but they somehow forgot to notice that it wasn't replaced by "Modified Galilean Epicycle Theory" or something of that sort.

Or more generally, their style of writing ignores that most of the alleged crackpots really are crackpots.