at net.minecraft.server.v1_4_6.ThreadServerApplication.run(SourceFile:849) [
at net.minecraft.server.v1_4_6.MinecraftServer.run(MinecraftServer.java:416) [
at net.minecraft.server.v1_4_6.MinecraftServer.q(MinecraftServer.java:481) [
at net.minecraft.server.v1_4_6.DedicatedServer.r(DedicatedServer.java:224) [
at net.minecraft.server.v1_4_6.MinecraftServer.r(MinecraftServer.java:585) [
at net.minecraft.server.v1_4_6.DedicatedServerConnection.b(SourceFile:30) [
at net.minecraft.server.v1_4_6.ServerConnection.b(SourceFile:39) [
at net.minecraft.server.v1_4_6.PlayerConnection.d(PlayerConnection.java:112) [
at net.minecraft.server.v1_4_6.NetworkManager.b(NetworkManager.java:290) [
at net.minecraft.server.v1_4_6.Packet3Chat.handle(Packet3Chat.java:44) [
at net.minecraft.server.v1_4_6.PlayerConnection.a(PlayerConnection.java:852) [
at net.minecraft.server.v1_4_6.PlayerConnection.chat(PlayerConnection.java:908) [
at net.minecraft.server.v1_4_6.PlayerConnection.handleCommand(PlayerConnection.java:990) [
at org.bukkit.craftbukkit.v1_4_6.CraftServer.dispatchCommand(CraftServer.java:554) [
at org.bukkit.command.SimpleCommandMap.dispatch(SimpleCommandMap.java:186) [
at org.bukkit.command.PluginCommand.execute(PluginCommand.java:44) [
at com.thevoxelbox.voxelsniper.VoxelSniper.onCommand(VoxelSniper.java:234) [
at com.thevoxelbox.voxelsniper.VoxelSniperListener.onCommand(VoxelSniperListener.java:64) [
at com.thevoxelbox.voxelsniper.VoxelSniperListener.commandSniperB(VoxelSniperListener.java:137) [
at com.thevoxelbox.voxelsniper.Sniper.setBrush(Sniper.java:674) [
at com.thevoxelbox.voxelsniper.brush.perform.PerformBrush.parse(PerformBrush.java:38) [
at com.thevoxelbox.voxelsniper.brush.OverlayBrush.parameters(OverlayBrush.java:172) [
at java.lang.Integer.parseInt(Unknown Source) [
at java.lang.Integer.parseInt(Unknown Source) [
at java.lang.NumberFormatException.forInputString(Unknown Source) [
java.lang.NumberFormatException: For input string: "" [
2013-01-19 20:27:55 [SEVERE] null
(TheFeli Overlay (Topsoil Filling)) par [ over d 3 ]
2013-01-19 20:27:55 [WARNING] [VoxelSniper] Exception while receiving parameters:
2013-01-19 20:27:55 [INFO] TheFeli issued server command: /b over d 3

No information and an incomplete stacktrace. Well done.

Also my guess is, that you are using the depth parameter wrongly... it's d3 not d 3