The Old System (pre-1.3)
To fully understand the various wards, you should read this article. Basically, wards are used to gate progression and can be found on various gear sets. Once you reach the endgame, you need Lesser Wards to stand a chance against mobs in the city dungeons and RvR fortresses. You need Greater Wards to be competitive against Lost Vale mobs and Stage 1 city public quest bosses. And so on. To gain the benefits of wards, you must be wearing gear that grants them. Wards do not impact RvR.
Currently, tier 4 players have a few ways to gain competitive gear. They can take the PvE route, which includes quests, lairs, and dungeons. The first two options do not grant warded gear, but some of the items are actually pretty good. Of the dungeons, players can enter Bastion Stair to gain Lesser Ward, city dungeons for Greater Wards, and Lost Vale for Superior Wards.
Players can gain ward gear three ways from RvR. When killed, players will sometimes drop a warded item and the quality of that item will depend on their renown rank. Players, keeps, fortresses, zone locks, and city PQs grant tokens of varying quality, which can be traded in for warded gear of your choice. Finally, keeps, fortresses, and city PQs randomly award gold bags, which include warded gear.
There are two problems with the old ward system. First, the various wards are only available on gear that is part of a set and sets grant large set bonuses (e.g. wearing 2/5 pieces gives +XX to StatA and wearing 3/5 gives +XX to StatA and +YY to StatB).
Second, you must be wearing your warded gear to receive the ward bonus. If you are not wearing warded gear, certain high ranking mobs will rip you apart. This may not immediately sound like a bad thing because sets are so good to begin with, however, both these factors combined lead to a major drawback of this system: gear homogenization.
Given the benefits of wards and the fact that the sets grant such large set bonuses, the only gear worth wearing in WAR is part of a set. This makes for an extremely uniform and boring gear system that lacks flavour, customization, or diversity. Actually, it makes it very endgame WoWish, which seems odd since WAR's set out to attract those who are sick of World of Warcraft and its gear treadmill especially.
Sigils, vessels, and tokens aim to fix this issue in patch 1.3.