The Gist: The 2000 Presidential Election between George W. Bush and Al Gore came down to Florida, where the tally was so close (a difference of 1,784 votes in favor of Bush) that Gore demanded a recount. While the recount was taking place, the Supreme Court put a halt to it, ruling a recount would violate the Equal Protection Clause of the Fourteenth Amendment, effectively making George W. Bush the next President of the United States.
This is one of the most controversial and convoluted decisions in U.S. Supreme Court History. For a complete breakdown, I would recommend good old Wikipedia, because the twists and turns of this situation were complex and long enough for books to be written about it. Essentially, however, the Supreme Court ruled a recount would be unconstitutional because different counties were using different standards of counting (treating voters differently), violating the Equal Protection Clause of the Fourteenth Amendment.
There are substantial problems with what the Court did. First, it was premature for the Court to hear the case to begin with; had the recount confirmed Bush the winner, the entire thing would have been a non-issue. By halting the recount, the Court unnecessarily brought a lot of illegitimacy to its own decision, Florida's results and as a consequence, the entire presidency.
By ruling that different standards of counting in different counties violated the Equal Protection Clause, it is hard not to wonder how it is, then, that every single state's election standards do not violate the constitution.
There are also valid arguments that the Court stuck its nose in other branches' businesses. The Court made a lot of decisions concerning Florida state laws that should have been reserved for the Judiciary of Florida and a lot of decisions concerning the election process that should have been reserved for the federal and local executive branches.
The majority was also hypocritical--many of the conservative justices who were a part of the majority opinion have consistently criticized other liberal justices for "judicial activism" (rulings based on personal or political consideration instead of the law) in cases where the conservative justices have ended up on the losing side. I do not know of a better example of judicial activism than the Supreme Court choosing who the next President of the United States is going to be.