A Spark Shot (also called an R-Shot) refers to a Charge Beam shot while shinesparking. Normally the game doesn't allow the player to shoot during a shinespark, but pressing R to release a Charge Shot bypasses this. This requires a full charge; if you try to shoot with a partial charge stored, nothing will happen.
Spark Shots are typically used to open doors while sparking on long straightaways, like the Elun or Hanubia bridges. To get the most timesave, you want to shoot early enough that the door has time to open before you hit it, but late enough that your shot doesn't despawn before hitting the door. If you do this perfectly, you'll be able to spark into the next room. It's helpful to learn a visual cue for each place you want to do this.
Spark Shots can also be used in places where hitting the door with the spark is unavoidable. The door can still be shot during the recovery animation from the shinespark, letting you immediately move onto the next room after it finishes. This is primarily done immediately after spark shooting another door, where there's no time or space to open both doors.
If the charge shot is fired before the shinespark, it won't reach whatever you're sparking towards, but firing it mid-spark gets it there with the right timing.
When heading left intending to leave Elun, you can save time by Spark Shooting the door to enter the save room while still sparking.
When heading right from the Ghavoran->Hanubia tram, you can save time by Spark Shooting the door to enter the save room while still sparking.
When speedkeeping through the frozen section of Artaria, the door dividing the Cold area from the Temperate area can be shot while speedkeeping using a Spark Shot, allowing the speedkeep to be extended without having to release any buttons.
Spark Shooting is possible because you cannot release a charged shot by just releasing the Y button during a shinespark. However, due to a programming oversight, switching to the Missile Launcher releases the charged shot under almost any circumstance, including a shinespark, despite being able to shoot neither charged shots nor missiles while shinesparking.