My single issue with vaccines, now that thimerosol has been eliminated, is the use of aluminum in them as an adjuvant despite the fact that aluminum is a known neurotoxin. There no conclusive science that states that it's use in vaccines is safe (there are peer reviewed, scholarly papers written on this very subject).
Even still, it's all we have against shit like Polio and the like, so I roll the dice with them. The only one I'm 100% against is the flu vaccine, 'cause it doesn't always work, so what's the point?