Still, sometimes you really do have to report your boss to Human Resources or someone in management. Here are four times where you're legally protected from retaliation if you complain (no, I can't guarantee they won't retaliate anyhow, but you have some legal remedies if they do).
1. Discrimination/discriminatory harassmentIf you've been discriminated against due to your race, age, sex, pregnancy, religion, national origin, color, disability, genetic information, or another category that's protected in your state/county/city (e.g., marital status or sexual orientation that aren't protected by federal law), then you are legally required to follow your employer's published discrimination/harassment policy and report it. If you don't, then you may be giving up your right to sue for discrimination.
2. Wage/overtime violationsIf you object to the company's failure to pay wages owed or failure to pay overtime, you may be protected from retaliation under the Fair Labor Standards Act or your state's wage/hour laws.
3. Illegal activity of the companyIf the company is violating the law -- Medicare fraud, ripping off the government, failing to pay taxes, failing to pay wages, discriminating, polluting, etc., there are a host of whistle-blower laws that may protect you. You need to find out which law protects you and make sure that you complain in a way that's protected. Some laws require you to complain in writing to a supervisor. Some say that you have to report the company to a government agency. Some only require that you object to or refuse to participate in the illegal activity. If you get it wrong, you aren't protected from retaliation.
4. Collective action to improve working conditionsThe National Labor Relations Act protects employees from being retaliated against if they get together to try to improve the terms and conditions of their employment. So those letters that employees sometimes write to complain against unfair treatment or bullying are supposed to be protected. Your remedies under this law aren't the easiest to get or the best, but it's something to hang your hat on and wave in front of the boss if they start threatening retaliation.
If you're going to complain, I suggest putting it in writing even if the policy says to have a meeting. You can present the written document at the meeting. That way you have proof that you complained about something that's protected. Otherwise, HR will likely say you complained about general harassment or unfair treatment, which isn't protected. If you do decide to complain, keep it professional and to the point. Avoid complaining about personality conflicts or incompetence. Stick to the facts that prove that what's happening is illegal.
HR is entitled to investigate your complaint. That means that even if they have a policy of keeping your complaint confidential, your boss, the person you're complaining about, and your witnesses and other coworkers will probably find out about it. Be prepared for that to happen, and be ready to report retaliation.