Minecraft Vanilla Servers
Minecraft Vanilla servers are all servers that are running Minecraft server software without gameplay modifications. Some servers would even run Vanilla Minecraft server without any mods at all.
Are all Minecraft Vanilla servers the same?
Not necessarily, even Vanilla Minecraft servers software provides some settings that can impact gameplay, such as keep inventory, mob griefing and more on top of that, some Vanilla Minecraft servers would have their own set of rules, which means you're not free to do whatever you want as those are not Anarchy servers.
Bukkit/Spigot Vanilla servers?
Not all but most of Vanilla Minecraft servers nowadays are generally using Bukkit/Spigot software mainly for performance reasons. If you're looking for pure Vanilla Minecraft server be sure to check which software the server is using.