The current protocol version is 0x01.  The maximum packet length is 511 bytes.

(BYTE) protocol version
(BYTE) packetid
(SHORT) packetlen
(...) DATA

Current packets:
(send to server) id 0x00: keepalive
(NO DATA) --- there is no response to this packet.  You should send this once every 2-3 minutes.

(send to client) id 0x00: keepalive
(NO DATA) --- the server sends this to the client when the connection has been idle.  No response is needed.

(send to server) id 0x01: log on to botnet
(STRING) bot id
(STRING) hub password

(send to client) id 0x01: log on status
(DWORD) status (0 FAIL 1 OK)

(send to server) id 0x02: update bot stats
(STRING) unique username on battle.net
(STRING) current channel on battle.net
(DWORD) battle.net server ip
(STRING) database id (which database to use) * also now includes database password.  Use the following format: "name password".
(DWORD) cycle status (0 NOTCYCLING 1 CYCLING)

(send to client) id 0x02: update bot stats status
(DWORD) status (0 FAIL 1 OK)

--

(send to server) id 0x03: database modification
(DWORD) command
command 1: request user database
command 2: add a database entry/modify a database entry
(STRING) usermask
(STRING) flags
command 3: remove a database entry
(STRING) usermask

(send to client) id 0x03: database change
(DWORD) command
command 2: new access list user/modify existing access list user
(STRING) usermask
(STRING) flags
command 3: remove a database entry
(STRING) usermask

--

(send to server) id 0x04: command to bots on same database
(STRING) sending user
(STRING) command

(send to client) id 0x04: command over botnet
(STRING) sender
(STRING) command

(send to server) id 0x05: cycle request
(DWORD) count
(STRING LIST) usernames of bots to cycle

(send to client) id 0x05: cycle request notification
(STRING) channel to cycle

(send to server) id 0x06: request information about bots on botnet

(send to client) id 0x06: botnet bot information
(DWORD) bot id
(STRING) bot name
(STRING) bot channel
(DWORD) bot server

(send to server) id 0x07: command over botnet to all botnet bots (send 0x04 to client)
(STRING) sending user
(STRING) command

(send to client) id 0x07: bot disconnecting from botnet
(DWORD) bot id

(send to server) id 0x08: command to specific botnet bot (send 0x04 to client)
(DWORD) target bot id
(STRING) sending user
(STRING) command

(send to server) id 0x09: change database password * Requires 'full' access
(DWORD) password to change (0: readonly, 1: full, 2: restricted)
(STRING) new password

(send to client) id 0x0a: botnet server version
(DWORD) version --- current version '1'.  This will change when new features are added.  Thus, you will know what features a particular botnet server supports right away.  This is sent before logon confirmation.
Version information:
Version 1 supports all packets 0x00 through 0x0b.

(send to server) id 0x0b: botnet chat
(DWORD) command --- 0x00: message to bots on the same database, 0x01: message to all bots, 0x02: message to bot specified by id.
(DWORD) action --- 0x00: talk, 0x01: emote
(DWORD) id --- for command 0x02, id of bot to send to, otherwise ignored.
(STRING) message --- chat message to send.

(send to client) id 0x0b: botnet chat
(DWORD) command --- 0x00: message to bots on the same database, 0x01: message to all bots, 0x02: message to bot specified by id.
(DWORD) action --- 0x00: talk, 0x01: emote
(DWORD) id --- id of source bot (for all commands)
(STRING) message --- chat message sent.