Vanilla
The official Minecraft server software. No plugins, no modifications. Ideal for purist servers but has significant performance limitations at higher player counts.
CraftBukkit
The original plugin platform. Now largely obsolete — use Spigot or Paper instead. Still the API foundation that everything else builds on.
Spigot
The most popular Minecraft server for years. Adds performance improvements over Bukkit and runs all Bukkit plugins. Still widely used but Paper offers better optimisation.
Paper
The current recommendation for almost all servers. Significant TPS improvements, async chunk loading, better memory usage, and excellent developer APIs. Runs all Spigot and Bukkit plugins. CraftNodes installs Paper by default.
Purpur
A fork of Paper with extra configuration options and fun additions. Fully compatible with Paper plugins. Great for servers that want more control over vanilla behavior.
Which to Choose?
Use Paper. It has the best performance, the best community support, and the most active development. The only reason to use vanilla is if you explicitly want no modifications whatsoever. CraftNodes defaults to Paper and supports switching to any other server type via the Pterodactyl startup settings.