It is such a personal decision.
I had the flu vaccine while in my 3rd trimester with Phoebe (because she'd be born in flu season). The swine flu vax is the same as the flu vax, but with an added ingredient (the dead swine flu virus), so if it were me, I'd have it. The flu vax changes every year - they add a more current strain. Personally, I trust it. But everyone is different.
I am more afraid of the illnesses than vaccines.
The fever is the thing to worry about, as high temperatures can have a harmful affect on the fetus. So if you feel yourself getting ill with a temperature, make sure you see to it.