See http://mod-buildcraft.com/forums/index.php?topic=559.0. I can reproduce with the following trace:

net.minecraft.util.ReportedException: Ticking block entity
at net.minecraft.server.MinecraftServer.updateTimeLightAndEntities(MinecraftServer.java:703) ~[MinecraftServer.class:?]
at net.minecraft.server.dedicated.DedicatedServer.updateTimeLightAndEntities(DedicatedServer.java:341) ~[DedicatedServer.class:?]
at net.minecraft.server.MinecraftServer.tick(MinecraftServer.java:608) ~[MinecraftServer.class:?]
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:482) [MinecraftServer.class:?]
at net.minecraft.server.MinecraftServer$2.run(MinecraftServer.java:746) [MinecraftServer$2.class:?]
Caused by: java.lang.NoSuchMethodError: net.minecraft.entity.item.EntityItem.setVelocity(DDD)V
at buildcraft.transport.PipeTransportItems.dropItem(PipeTransportItems.java:377) ~[PipeTransportItems.class:?]
at buildcraft.transport.PipeTransportItems.moveSolids(PipeTransportItems.java:294) ~[PipeTransportItems.class:?]
at buildcraft.transport.PipeTransportItems.updateEntity(PipeTransportItems.java:264) ~[PipeTransportItems.class:?]
at buildcraft.transport.Pipe.updateEntity(Pipe.java:193) ~[Pipe.class:?]
at buildcraft.transport.TileGenericPipe.updateEntity(TileGenericPipe.java:301) ~[TileGenericPipe.class:?]
at net.minecraft.world.World.updateEntities(World.java:2116) ~[World.class:?]
at net.minecraft.world.WorldServer.updateEntities(WorldServer.java:528) ~[WorldServer.class:?]
at net.minecraft.server.MinecraftServer.updateTimeLightAndEntities(MinecraftServer.java:697) ~[MinecraftServer.class:?]
... 4 more

That will call for a hotfix release...

sugestion: take a soldering iron and weld the pipes so the item can't get out? =p

This setVelocity name is really not appropriate. But anyway, the fix was straightforwards. Will release 6.0.10 soon, maybe tonight, maybe tomorrow.