Hi K.,
I'm not sure if you're speaking about the regular flu vaccine or the swine flu vaccine (or both!). Both are made the same way -- the same "formula" is used to create a vaccine containing antigens from the flu viruses expected to be the most common this year (or with the H1N1 antigens, in that case). If you get the injection, the virus in the vaccine is totally and completely dead -- it should not be able to give you the flu under any circumstances (the nasal spray vaccine contains live attenuated virus so it could at least theoretically still mutate and make you sick). Also, the single-dose injections do not contain thermerisol (mercury), so if you're worried about that, you should request that kind rather than an injection from the multi-dose vial.
Although each year's particular batch of the vaccine is made new, the formula has been used for decades and I believe is well-tested at this point. There are always risks with anything, of course -- people could have allergic reactions to it and there seems to be about a 1/1,000,000 chance of getting Guillian-Barre syndrome from it, per cdc.org. On the other hand, if your child gets the flu (H1N1 or regular flu), his chances of dying from the virus are higher than his chances of complications from the vaccine.
I am generally pro-vaccination -- although I personally prefer a delayed schedule -- but I can go either way on the flu vaccine. I think that's because the vaccine doesn't protect you against all kinds of the flu and because the flu generally more miserable (albeit very, very miserable) than it is dangerous. Personally, if my child stayed home most of the time, I might opt not to get it until school-age ... if he were in daycare, I think I'd get it. Good luck!