Yeah, as already stated (implied), within Tokyo area Marunouchi and Ginza lines are the only lines using a third-rail. I think some others are in Kyoto-Osaka area, but this is "imported technology" that was discontinued once the Japanese were building their own lines without foreign assistance. The Oedo Line is new but also incompatible, using (semi-)linear-motor technology. Almost all lines are narrow-gauge (subways and shinkansen are standard gauge), excluding new transit systems (yurikamome) and monorails. The Keio Line uses some absurd gauge found nowhere else in the country, but Toei built a subway line (Shinjuku line) with the same gauge for the express purpose of running through service on Keio (I beleive this is one of the pioneers of the through service schtick). Other weird gauges include the Tokyuu Setagaya Line (Wide gauge), and probably the Toden Arakawa Line (Kanto's only streetcar line). However, due to a railway nationalization law that has been in effect for just shy of all hundred years now, lines are almost a narrow gauge. While there are lines that differ in the AC and DC power supplies, many rolling stock now are compatible with both and thus are not an issue for through-service operations.AG said:The vast majority of the trains that operate in Tokyo are electric multiple units (EMUs) that draw power from catenary power lines from above the tracks. In the case of third rail, power is drawn from beside the track. Not only that, the voltage provided to each power system is often different, and some are AC powered while others are DC. Making them compatible would require quite a lot of work with trains (eg. adding pantographs).
Some lines are also not compatible because of the numerous gauges used on some Tokyo rail lines. A lot of them, particularly the JR East lines operate the 1067mm narrow gauge.
The main thing with third-rail though, is that through-service operations are on surface rail networks, which include at-grade corssings, which is impossible with third rail (not safe is an understatement).