Below are some examples from a contemporary American view. These mechanisms wouldn't have be applicable if you were interested in the view of the Ancient Greeks, who were very concerned with this subject.
Indirect Elections
In America, the people do not directly elect the President. We elect representatives to elect the President. The elector has no other function besides electing the President. This can provide some insulation against the will of the majority, because the representative can vote contrary to the popular will. Of course, this doesn't typically happen, but it is one mechanism in our system designed for exactly this purpose. In fact, historically the United States Senate was also selected indirectly, but this changed with the 17 Amendment.
Wikipedia maintains a list of other indirect elections.
Legislative Authority
In most of the world's democracies today, the people cannot directly legislate. Instead, they elect legislators who create laws for them. This is a large check against the majority: in any given election, they could lose.
This specific issue was one of the ancient Greek's main concerns, since they often exercised direct democracy.
In practical terms, depending on the size of the majority and their specific election rules they may not have to worry about this. However, in other cases it will be a significant deterrent.
Judicial Independence
Judges in America are designed to be insulated from politics. As such, they should be aloof from the will of the majority. There are many specific mechanisms for this including: being appointed (rather than elected), appointments are for life, judges do not report to a political body (such as a legislature or executive department), and an independent professional body (typically a bar association).
Judicial independence is critical for the rule of law. It's what allows a judge to rule based on the merits of the law, rather than political circumstances or the majority's will.
Election Terms
A short election term provides incentives for a representative to obey their electorate. A long election term provides more freedom. This is the reason why the Senate is given a six-year term, but the House of Representatives is only two years. Similarly, judges are appointed for life which provides them the maximum insulation from politics.
The Party System and Electoral Structure
The party system exists to aggregate the wants of many disparate groups. The structure of elections and the party system can be limit the influence of the majority, or enhance it. For example, in America party elite control legislative committee assignments and much of the funding for campaigns. This isn't directly controlled "by the people" and may be freely dispensed regardless of the majority's will.
Conversely, the winner-take-all system in America gives the majority a big advantage. Here, a candidate wins an election by having the majority of votes in that area. Votes are not split based on the proportion of votes in that area they receive. This benefits the majority by allowing them to easily repress even fairly sizeable showings by minority parties.
Legal Protections
Most democracies have (either through their Constitution or legislation) minimal legal protections for all citizens. For example, the United States Constitution guarantees the freedom of the press. This protection prevents the majority from directly shutting down media which they disagree with. Of course it only really works if the courts agree and other institutions play ball too.
Additionally, they may have protected categories which may not be discriminated against. These laws prevent the majority from abusing the minority, at least as long as the laws stand.
Rule of Law
The rule of law prevents power from being used improperly by restricting the authorized usage of power. For example, although the Supreme Court can overturn laws (a powerful feature), they can deal with laws that are brought before them. These laws effectively restrain governmental officials.
As long as these rules and procedures are followed, there are a lot of checks to exercising power. Each of these rules is a barrier to arbitrary uses of power by the majority.
