The false associations, such as the story above about "rheumatiod arthritis, a chronic condition due to an extra strength flu shot" are wrong - coincidence at best. There is NO medical evidence that this is the case. Side effects are one thing, people often experience a couple of days of achiness or fever. This doesn't trigger diseases, but people look around for something to blame when they receive a traumatic diagnosis and proximity to an immunization is a popular scapegoat.

Via a WebMD query:

It's not uncommon to feel some soreness, redness or swelling in the area where you had the shot. It lasts 1-2 days. It's rarer, but, you may have a brief fever, feel achy all over, have a headache or feel tired for 1-2 days.

About one in every million flu shots leads to a severe side effect. The best known is a disease that affects the nerves and brain, called Guillain-Barré syndrome.

But the chance of severe complications from getting the flu is far higher than the chance of complications from the flu shot. The flu can lead to pneumonia and heart attacks. It can also lead to conditions of the nerves and brain, including Guillain-Barré syndrome. In fact, this illness is more likely to happen after the flu than after a flu shot.

One of my family members has some immunity issues (if you're missing a spleen you have one less tool to fight illness) and is supposed to get a flu shot every year. I do so also, to be less likely to infect that party.