Anime series are notorious for having strange and seemingly random titles. The popular medium of Japanese animation has spawned shows with names ranging from Cowboy Bebop to Martian Successor Nadesico to Fullmetal Alchemist -- each more peculiar than the last. If you're creating your own anime, or simply enjoy brainstorming for hypothetical anime series titles, there are several ways to come up with a name that's fitting, yet still contains that odd spark of whimsy so often found in anime titles.
Follow the naming conventions of existing anime series. The majority of existing anime series are named after the show's protagonist: Naruto, Sailor Moon, and Hellsing are some well-known examples. Major plot points are also often used as titles. Death Note, for example, features a notebook that causes the death of anyone whose name is written in it. Look at the list of titles on a website like Anime Nfo for inspiration.
Give your anime a title in Japanese, if you know the language, and then translate it into English. Many anime series have unusual names because of difficulties in translation, or because of the poor English skills of translator. Hagane no Renkinjutsushi, the Japanese name of Fullmetal Alchemist, for example, literally translates as "Alchemist of Steel." The Japanese words "Shin Seiki," translated as "Neon Genesis" in the title of Neon Genesis Evangelion, would normally be translated as "New Beginning." Try to think like a native Japanese speaker as you make the translation.
Use an automatic online anime title generator tool if you just want to come up with a fun name with as little effort as possible. The website Lance and Eskimo has a fast and simple title generator, and Seventh Sanctum has several powerful anime-related generators capable of creating as many titles, character names, descriptions, and plot twists as you need.