Hi,
When the Bujinkan was first formed (70's/80's), Hatsumi Sensei used the Togakure Ryu name as an umbrella term for everythig he taught (from all the systems he inherited from Takamatsu Sensei). This is most often thought to be because Togakure Ryu has the longest tradition (34 Sokes, founded 1185), and was therefore given more respect than the other arts. However, the main technical knowledge came from systems such as Gyokko Ryu (Kihon Happo and Sanshin no Gata), Takagi Yoshin Ryu (the basis of most of the Bujinkan's Muto Dori), Kukishinden Ryu (most of the weaponry techniques: sword, bo, hanbo, etc) and a few others. So even when the earlier practitioners had their ranking in Togakure Ryu, it was really still a "Bujinkan" rank under a different name. This isn't an uncommon situation, though. The Shindo Muso Ryu Jojutsu includes arts such as Ikkaku Ryu Juttejutsu, Uchida Ryu Tanjojutsu, Isshin Ryu Kusarigamajutsu and Ittatsu Ryu Hojojutsu; the Yagyu Shinkage Ryu in some branches include a separate Iai school called Yagyu Seigo Ryu.
For Togakure Ryu's physical techniques, the scroll is broken into a few different sections, and is covered in other threads here... but in short, the main scroll includes the Santo Tonso no Gata (defences against grabbing and weapon attacks, using Metsubishi and Senban Shuriken), the Ukemi no Gata (Shuko against sword), Hiden no Gata (intuition/Sakkijutsu), Shinobi Gaeshi Gata (concealed techniques), as well as sections on Kamae, and a scroll of swordsmanship. This year for the Bujinkan is the year of Togakure Ryu, so there will probably be a fair amount of information coming out as the months go on, and Hatsumi Sensei has a new book out soon which is supposed to include the kata for each and every school that is taught.
For other Ninjutsu schools... it really does depend on your interpretation. The Gyokko Ryu, Koto Ryu, Gikan Ryu and Gyokushin Ryu have very closely related histories, and have been linked with the Iga region of Japan, as well as with prominent Ninja of history (such as Momochi Sandayu, who is claimed as Soke of Gyokko Ryu and Koto Ryu, and Ishikawa Goemon, who was said to have been a student of Gyokko Ryu, although the Ryu doesn't mention him as far as I know), so you could claim them as Ninjutsu Ryu. Add to that the Kumogakure Ryu, which is thought by some to have been developed by the Toda family when they were the heads of Togakure Ryu, using Togakure Ryu as a basis. Not much has been shown of Kumogakure Ryu (see Hatsumi Sensei's Koppojutsu DVD for perhaps the only example), but it is said to have very few kata, being more based in strategies than physical movements, but does include such "secret weapons" as Ippon Sugi Nobori and the Kama Yari.
Most of the other elements (Bajutsu, Tenmon Chimon, Kyujutsu etc) seem to be things that you would cover in your own personal research. I seem to remember reading years ago Hatsumi Sensei saying something along the lines that the old ways of predicting weather aren't that important these days, as the news each night gives a pretty good idea using their satelites and modern technology. But that doesn't mean that the old knowledge isn't there...
Lots of taijutsu, weapons, and other neat stuff... Check out 
<poor me>
