As with all things, some are good, some are bad. You can't blanket all of them in one light, and you should definitely research rather than just blindly handing out money. However, I know/have worked with several charities that do very good and very important work. Many local-level charities are more hands-on than big, corporate-style affairs. I've worked closely with a couple of womens' shelters, and these people are flat-out amazing. The things they do for battered/abused women and families is just astounding...from getting them out of dangerous situations to helping them with school/jobs so they can move towards independence. And most are fairly low-key as far as fundraising. They usually don't advertise themselves, but rather rely on word-of-mouth and the kindness of donors.
I'm also a strong supporter of several disease-based charities. Again, you need to make sure your money is going to the right place (i.e. hospitals) and not some CEO's bank account. But I've lose a few members of my family to currently incurable diseases like AIDS. We also have a family history of lupus (which I myself have to be repeatedly checked for, as symptoms can arise over time). Awareness should definitely be spread, and hopefully cures created.