Command, control, communications and intelligence (C3I) and intelligence, surveillance and reconnaissance, are two concepts that show the interplay of intelligence and operations in modern warfare. There are variants of both, such as C4I, which adds "computers", and ISRTA or RSTA, in which the TA stands for target acquisition.
Command is a lawful authority that sets goals, and has responsibility for, subordinate personnel, units, or other resources. Control directs the the actions of those resources, to carry out those goals, through the functions of control, or can delegate various levels of control.
Surveillance and reconnaissance are both means of intelligence collection, surveillance being a continuous process while reconnaissance is carried out by specific missions. In this context, intelligence analysis processes and analyzes the information generated from surveillance and reconnaissance, combining it with information already known. Strategic intelligence collection is more long-term.
Whatever the particular set of initials, the key message is that in modern warfare, the interaction of these functions need to be considered in building tools, techniques, and units. The various functions need to use compatible communications protocols, database organization, etc., which will allow sharing of information.
While the initial examples here will be from the United States, many of the definitions, and even the specific systems, are common in NATO, as well as with allied states such as Australia.
C3I-ISR information flow
Advanced militaries are constantly focused on improving the flow of information about the opponent and about the actions of one's own side. The former identifies the most effective weaknesses to exploit and the most dangerous capabilities to avoid, while the latter avoids fratricide while encouraging mutual support and efficient resource use.
In combat environments, C3I-ISR aircraft, which typically are large and have minimal self-protection, are high value units that require defensive fighter screens. Due, in part, to their vulnerability, there is a trend to put their sensors on unmanned aerial vehicles with control and analysis on the ground.
Evolution of U.S. C3I-ISR aircraft
At present, there are a great many types, which, in part, derives from a problem of physics: intelligence collection systems that listen for faint signals are apt to interfere with their own systems if they also generate powerful radar or radio signals. Most of these aircraft are under the functional direction of the United States Strategic Command, and operationally under the Eighth Air Force.
Current generation of strategic aircraft
|Airborne battle management and early warning radar
|E-8 Joint STARS
|Ground surveillance imaging radar
|EC-130 COMPASS CALL
|ELINT and COMINT in support of electronic attack (e.g., jamming)
|EP-3 ARIES II
|ELINT and COMINT
|Possibly anti-submarine warfare
|Possibly anti-submarine warfare
|RC-135 COBRA BALL
|MASINT on ballistic missiles
|RC-135 COMBAT SENT
|RC-135 RIVET JOINT
|No command, but often warns pilots
Challenging assumptions in a new generation of aircraft
Some new technologies may provide a way to challenge the self-interference problem:
- active electronically scanned arrays (AESA)
- Conformal antennas, where the physical shape of an antenna will not be limited to the usual radar domes, trailing wires, stubs, etc., but will be part of the exterior skin of the aircraft.
It's safe to say it will be a flying antenna — Ted Klapka, L-3 Communications liaison to Northrop Grumman
While the antenna technology is transferable, U.S. Secretary of Defense Robert Gates identified the EPX aircraft as a candidate for cancellation in the 2011 budget, as a program that was developing in a less than satisfactory way. 
The United States Air Force had planned the E-10 aircraft, to combine sensors and command & control. Although the project had its budget cut, the operational concept was to have an AESA radar that could do electronic intercept, but also disable "air-to-air and surface-to-air missiles with bursts of high-power microwaves as a self-defense capability. It would have the offensive capability of similarly disabling stealthy cruise missiles, as well, which it was capable of detecting at tactically useful ranges. The combination was dropped because it was deemed impossible due to cost and improbable due to technology restraints. As of Fiscal Year 2008, the E-10 project was cancelled.
Another version, proposed, in 2001, by Chief of Staff of the Air Force GEN John Jumper, was the MC2A, which could replace 33 E-3 Sentry, 17 E-8 Joint STARS and 14 RC-135 RIVET JOINT aircraft, with a single aircraft on a Boeing 767 airframe. This soon evolved to a less ambitious plan, in which two active radar functions, air surveillance on the E-3 and ground surveillance of the E-8, might be combined. Funding was obtained,however, only to try a ground surveillance aircraft, called Spiral 1, with the potential for growth. 
Spiral 1, however, would offer advances over the E-8, especially the Multi-Platform Radar Technology Insertion, a "Ground Moving Target Indicator (GMTI)" radar that was not limited to ground targets, as is the E-8, but could also detect low-level cruise missiles. Spiral 2 is the AWACS mission and Spiral 3 is the RIVET JOINT mission.
A new approach is to build on the P-8 Poseidon aircraft, which uses a Boeing 737 airframe. With the Littoral Surveillance Radar System, it can take on the function of the E-8 Joint STARS. Still, unmanned aerial vehicles play an increasingly important unit.
- Fulghum, David A. (22 February 2008), "U.S. Navy Plans EPX Intel-Gathering Aircraft", Aviation Week & Space Technology
- Jim Garamone (18 June 2010), Pentagon budget request reflects reform agenda: Defense Secretary Robert M. Gates testifies before the Senate Appropriations, American Forces Press Service
- Erwin, Sandra I. (July 2003), "Air Force to Run Wars From Sensor-Packed Jets", National Defense Magazine