Are we talking about an organized boycott, where you tell them what you're doing, and why, and enlist others? Or just a casual boycott, where you simply decline to do business with them?
These are the places I casually boycott, either due to principle, or because I want to help the market work, by punishing bad business practices:
Charmin, because I hate their stupid bear commercials, where they show me pieces of toilet paper, stuck to a bear's rear end.
The local mortgage place, because the owner used to annoy the Holy Hand Grenade out of me, with his stupid voice in the commercials.
Restaurants that serve alcohol.
Places I mostly boycott:
Places that go overboard with their sexy advertisements (Hardees, GoDaddy.com, European-American-Armory (also boycotting them for their embarrassing, robot-woman-with-gun-leg adverts - they should change their name to WTFJapan-American-Armory))
Local grocery chain that isn't posted, but has a history of victim-disarmament-activism