And in fact the line from Justice Holmes in Schenck v. United States is “The most stringent protection of free speech would not protect a man in falsely shouting fire in a theatre and causing a panic.” That “falsely” is what’s doing the work, both in Justice Holmes’s hypothetical, and in how such a false shout would be treated by First Amendment law today. Knowingly false statements of fact are often constitutionally unprotected — consider, for instance, libel, fraud, perjury, and false light invasion of privacy. That would presumably apply to knowing falsehoods that cause a panic. (Even given bit complicated by the Stolen Valor Act case, such knowing falsehoods that are likely to cause tangible and immediate harm are likely to be punishable, as the concurrence suggests.)
If the statement is not knowingly false, though, the analogy breaks down. The comment I linked to, for instance, used the “shouting fire” analogy to argue in favor of criminal punishment of speech that urges boycotts of Israel:
Spreading hatred that incites to violence is not what a free and civil society allows. The boycott movement specifically exists to single out the sole Jewish nation, delegitimize its existence and support the close to 70 year long war to destroy that nation.