Since the beginnings of what we would today recognize as Japanese culture, and probably earlier, various symbols, crests, banners, or markings on armor were used to help identify and distinguish warriors on the battlefield. The mon, or symbol, of a clan or a daimyo was particularly common, identifying which side a warrior fought on; some samurai used their own names or mon rather than that of their lord, while other factions, such as the Ikkō-ikki, could be identified by banners declaring namu amida butsu, praising the name of the Amida Buddha.
By the mid-16th century, flags and banners were seen in greater numbers than ever before, and in an unprecedented variety of styles, sizes, shapes and colors. Where once only higher-ranking samurai and commanders had standards (flags), now lower-ranking warriors wore flags to denote their unit or division, along with their clan or lord. Not only were armies larger than in the past, but the number of clans present on any given side in a battle had increased as well. In any one battle, a single daimyo could have under him several other daimyo, each with a number of units or divisions, and sub-commanders, as well as individual samurai of such a reputation (or wealth) as to warrant their own individual banner. This profusion of banners meant that the commanders, especially the daimyo at the head of each side of the battle, had to have especially large and noticeable standards to identify their location; warriors needed to know where to rally around, whose orders to follow, and what those orders were. The role of standard bearer was one of the most dangerous, and thus one of the most honorable, positions on the field of battle.
Gongs and bells were often used for related purposes, though these were rarely brought onto the battlefield. Rather, they would be kept at camp, and used primarily to rouse the army to battle, and to signal warnings of approaching enenmies and the like. It is rumored that in Uesugi Kenshin's war camp, the first bell meant to stop eating, the second to put on armor, and the third to move out onto the battlefield. Much like the Buddhist temple bells used for the same purpose in the Genpei War, later 'war bells' were bronze, and fairly large; they would be stuck by a wooden hammer from the outside, not by a clapper on the inside like Western bells.
Other devices, such as wooden clappers (hyoshigi) were sometimes used in urban war camps, or urban skirmishes, to set time and encourage troops. But the range of their sound is quite limited, and thus so was their use on larger battlefields.
Communications were, of course, not only necessary on the battlefield, but between battles as well. Takeda Shingen famously set up a system of fire beacons across his Province of Kai, so that he could be notified in the capital of Kofu as soon as his rival Uesugi Kenshin made a move. Wooden towers were filled with combustible material, and as each was lit, the next, some distance away, would see the signal and light theirs.
Once an army was on the move, scouts were often sent to provide reconnaissance, and messages needed to be transmitted between elements of the same army, or between allies, speedily, and without the information falling into the hands of the enemy. A number of systems of protecting their intelligence, and ensuring its safe delivery came about. Often, written messages would end with 'you will be informed of these things by the messenger.' By not placing the entire message in writing, the messenger could enjoy some degree of protection from those who would kill him and steal the scroll.
Attaching messages to arrows fired over a castle's walls was a common method of communicating with allies under siege. While the message was often simply wrapped around and tied onto the arrow, some used special arrows with hollow shafts specifically designed for this purpose. Whistling-bulb arrows, originally used just before a battle to draw the attention of the kami that they should watch the events about to transpire, were modified to serve as message-carrying arrows.