Bukkit 1.6 style logging log4j2 configuration (includes thread and log level in console and file) - Note that an update to log4j has caused the append parameter to be false by default. Also note that yet another update uses TerminalConsole instead of queue.

log4j2.xml

<?xml version="1.0" encoding="UTF-8"?>
<Configuration status="WARN">
    <Appenders>
        <Console name="WINDOWS_COMPAT" target="SYSTEM_OUT"></Console>
        <TerminalConsole name="TerminalConsole">
            <PatternLayout pattern="%highlightError{%d{yyyy-MM-dd HH:mm:ss} [%t/%level] %minecraftFormatting{%msg}%n%xEx}" />
        </TerminalConsole>
        <RandomAccessFile name="File" fileName="server.log" append="true">
            <PatternLayout pattern="%d{yyyy-MM-dd HH:mm:ss} [%t/%level] %minecraftFormatting{%msg}{strip}%n" />
        </RandomAccessFile>
    </Appenders>
    <Loggers>
        <Root level="info">
            <filters>
                <MarkerFilter marker="NETWORK_PACKETS" onMatch="DENY" onMismatch="NEUTRAL" />
            </filters>
            <AppenderRef ref="WINDOWS_COMPAT"/>
            <AppenderRef ref="File"/>
            <AppenderRef ref="TerminalConsole"/>
        </Root>
    </Loggers>
</Configuration>