Consistent and ongoing recon-probes continue to be launched into the US Infrastructure, including government and municipal systems. Boldly stated, all large Enterprises (government and corporate alike) are compromised by some form of malware that is CURRENTLY under C&C from a remote attacker. Malware infections are the tip of the spear - at the other end of an active malware C&C network is a human being or organization with intent and funding.
Recon-probes are malware implants that only scan ports and inventory the resources in the network, then phone home with the data. In many cases, probes are not targeted (not aimed only at your network, but rather like a shotgun approach) - there is an ongoing effort to simply map everything that sits behind the public gateways. In particular, probes have been launched into the US Infrastructure SCADA networks - think power grids and water plants.
Probes will be less complex than a full-blown botnet agent. One component to be on the lookout for is a TCP/IP-only capability - not something that injects into IE or Explorer, but rather a cleaner implant with a port scanning and sniffing capability. These probes will have a C&C backchannel of some kind, but are likely to store their information on disk for a while, as they don't phone home very often. These are forward probes designed to map your network. They may even query the hard-drive serial number via IOCTL's to the NTFS driver, this is for node identification decoupled from the IP address of the host. There will also be a query to see if the box has multiple interfaces.
If you find a probe operation, immediately assume that secondary attack tools have been brought into the network, perhaps in select subnets or on critical gateway machines. Be especially attentive to any sniffing capability on a collision domain near a gateway, or even on the gateway itself. In some cases, secondary capabilities have been dropped that have the ability to shutdown and destroy the computer. If you have captured a probe, immediately check all embedded registry keys and file paths for potential storage locations for secondary equipment.