Ball’s Bluff was a great episode about a battle involving less than 3,500 men, total. Latter in the war that would be a footnote to a campaign, possibly a skirmish. Ok a large skirmish, but you get my point. What battle with under 5,000 interest you and why are they significant?
I will start of with the Battle of Big Bethel, where General Magruder checked the Union advance in June of 1861 and it was not resumed until the Peninsula Campaign the next year.
Ball's Bluff looms large and is a good answer. The implementation of the Joint Committee on the Conduct of the War after the battle would have a large impact overall. Being early in the war and close to Washington also increased the magnifying glass on the battle.
The Battle of Hampton Roads may qualify if Naval battles are to be considered. The battle saw the Monitor and CSS Virginia square off in the first iron clad naval battle and brought about a Naval arms race between both sides.
A good conventional engagement to consider would be the Battle of Milliken's Bend in June 1863. Somewhat similar to the Holly Springs raid this was a Confederate attempt to break Grant's tenuous supply line from the Louisiana side of the Mississippi river. Unlike Holly Springs though the supply line was not broken and the Confederate force was held back. More importantly though the battle saw the prominent role of African American troops fighting for the Union. While not properly trained or equipped the soldiers fought valiantly for the cause, demonstrating to their peers, to Grant, and to the country at large that they were willing to stand up and fight. The Confederates were threatening to kill the soldiers if captured, the Confederate forces reportedly carrying a black flag into battle indicating no quarter would be given to prisoners. Also note that this battle occurred before the battle of Fort Wagner, popularized in the movie Glory.
Secretary of War Stanton would later write Lincoln of the courage shown by the African American soldiers, "Many persons believed, or pretended to believe, and confidently asserted, that free slaves would not make good soldiers; they would lack courage, and could not be subjected to military discipline. Facts have shown how groundless were these apprehensions. The slave has proved his manhood, and his capacity as an infantry soldier, at Milliken's Bend, at the assault upon Port Hudson, and the storming of Fort Wagner."
There's a little known battle/skirmish that took place in Pitt County, NC in 1862 as a part of Burnside's North Carolina Campaign. The battle of Tranter's Creek--with one Confederate Regiment & One Union Regiment with an additional Calvary unit---Initially, the Federal forces couldn't cross a bridge that was being defended by the Confederates, so Union Officer Lt. Col. Osborne ordered artillery fire. The Confederate commander was killed & the Confederates retreated. The Confederate unit was the 44th North Carolina led by Col. Singletary. & the Union forces were led by Lt. Col Osborne of the 24th Massachusetts. The Union was also accompanied by 3rd New York Calvary. The Union didn't pursue the retreating Confederates & marched back to Washington, NC. Though not much significance to the 1862 invasion of North Carolina---I went to school at East Carolina University in Pitt County. & though a lesser known battle, it still proves worthy of an interest to any student of the Civil War to pick up on a battle that they might not have known about.
& even though the Battle of Richmond, Kentucky was more than 5,000 men, I think it is often overlooked when it comes to significant battles.
---Michael