I used composted manure for years, and still do... just less of it. I always found that pig manure was best for growing tomatoes, and always had a hard time finding it. I talked to a guy who produced composted manure a couple of years ago, and he told me that the key is to get the temperature high enough in the compost to kill off the nasties (although I can't remember what he said his threshold was).
I also have to say that the Neptune's Harvest (fish/kelp) seems to be really working this year (first year I've tried it, and I was pretty skeptical).
Barry