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MySQL has an option to log all queries to a log file, stupidly though you need to restart the server to start/stop this log, its a bit lame, it also adds a lot of overhead to your box. I had the idea some time ago to use libpcap to figure out what gets sent to the server and started the code, I’ve mostly finished this now.
The MySQL protocol is undocumented but there is a reverse engineered protocol doc here. It is a tad outdated and I’ve found some queries that does not get parsed perfectly using the info there, I’ll look into those some more.
Here are some sample outputs from my code:

# ./mysqldump.pl -i mysql.cap
17:08:44: SET autocommit=1
17:08:44: SELECT last_insert_id()
17:08:44: rollback

It also has a more verbose option:

# ./mysqldump.pl -i mysql.cap -v
MySQL Packet:
Length          : 24
Packet Number   : 0
Packet Command  : 3
SQL Command     : SELECT last_insert_id()
Packet Header:
Source   : 192.168.1.1
Dest     : 192.168.1.2
S.Port   : 47241
D.Port   : 3306
Length   : 77
Timestamp: 1150128523.750337

I could make the script do its own dumping using libpcap it’s pretty easy but I prefer to only let it read tcpdump files, we get a LOT of queries (> 600 per second) and I don’t want slow perl code to affect the servers, tcpdump is pretty fast and efficient.
I use Net::Pcap and NetPacket::TCP to extract the packets from the file, decoding the MySQL commands is pretty easy then:

$plen = ord(substr($pkt, 66, 3));
$pnum = ord(substr($pkt, 69, 1));
$pcmd = ord(substr($pkt, 70, 1));
$cmd  = substr($pkt, 71);

The offsets etc is defined in the documentation linked too above, $cmd will now hold the actual query ran against the server, but only where $pcmd == 3.
I’ll upload the code for this in the next few days just letting a few people do some beta testing for me first.
UPDATE: You can now get the code here.