The problem I have with anti-vaccination claims is that they tend to be just collections of general negative information about vaccinations, as opposed to concrete hypotheses that people can test. To me, it looks like the kind of logic where you start with the conclusion and work your way back. The autism connection is an example of a concrete claim that they can test, and as far as I know, they can't find a casual connection.
Regarding the link to the Austrialian medical clinic, the fact that the vaccines aren't permanent doesn't necessarily mean that they aren't helpful when they are given. For instance, babies are heavily vaccinated because they are far weaker than healthy adults so they can't tank acute illnesses as well. If adults don't get exposed to a treatable illness very often, it's probably more trouble than it's worth to keep them vaccinated. One way they do get exposed is via travel to new places, hence the advertisement for the clinic's services.
Regarding the conflict of interest, it doesn't surprise me, but it doesn't really say anything specific about the vaccines themselves.
In the Oxford link, the listed results of the study only speculate causes. The only speculated cause that might contribute to an anti-vaccination case is that "Receipt of TIV could increase influenza immunity at the expense of reduced immunity to noninfluenza respiratory viruses, by some unknown biological mechanism." All this means is, if that really is the reason why the numbers came out the way they did, then this specific vaccine, in addition to preventing you from getting the flu, might also make you more susceptible to other respiratory viruses, probably for around the same amount of time that the vaccine works.
That's my best guess anyway, I have no medical training whatsoever so take everything I say with a truckload of salt. I'm all for independent research on medication, I do it for everything because I always end up with horrible doctors. The problem with the vaccine controversy is that it's tied up in theoretical, technical medical research, and when it comes down to the yes or no question of "do I vaccinate my kid", well, sometimes perfect is the enemy of good.
