Sorry about all these immature comments. Vanilla is a Minecraft server that is downloaded from minecraft.net, and it is pure without any mods. A Bukkit server is... well a Bukkit server.
OP was asking why a vanilla server is called vanilla,the reason for it.
Seriously you know nothing don't you? vanilla means pure and for example on your vanilla ice cream you can mix it with anything else like chocolate,etc.vanilla term is used in other games i played too
ironically you were just telling about something that OP already knows,unsurprisingly though
Vanilla is (incorrectly) seen as a bland and unexciting flavor, irl. This is probably a result of very low quality, cheap imitation vanilla extracted via alcohols which -is- quite bland and lacking any real depth of flavor.
REAL vanilla bean extract is a highly exotic thing, harvested from rain forests around equatorial regions. The pods are long and green, and require expert curing to develop that dark, rich depth of flavor that genuine vanilla extract has. The extract and inner lining of the pod and beans are quite valuable and thus, any product made with them tends to be very costly; hence why imitation vanilla became the standard.