This is not an April Fool's prank. Or well: the reason the site updated is because of April Fools, sure, but the point is, I'm not pulling your leg. Homestar Runner has updated for the first time in three years.
The update runs with the idea that people have been pestering Homestar Runner about when he'd update the site's most popular feature—which he takes to mean the "Hairstyle Runner Gallery," for whatever bizarre reason. Don't worry though, he updates other things, too. Strong Bad also makes an appearance, and you can even download his Windows 98 theme.
Ah, memories. Now to wait another ??? years until we get another update.