Federal law (as opposed to State law) applies. Some cases may be filed in either Federal or State Court. The decision is solely up to the prosecutors. In very rare cases a person may be prosecuted in both Federal and State court.
Federal Cases are often much more complex and require more time to prepare than State Cases.
Sentencing in Federal Court is determined by the Federal Sentencing Guidelines. Federal Judges have much less discretion in determining an appropriate sentence because of the Sentencing Guidelines, which often include mandatory minimum sentences.
In Federal Court, there is much less latitude in plea bargaining and the judge (Federal Magistrate) very seldom gets involved in plea negotiations.