Well, I can only go by my experience of what caught my eye.
1. For Mecha: Mobile Suit Gundam - all series. You will find that the majority of all the Gundam storylines have something to do with a character or situation from another Gundam series. My suggestion would be to watch them all so when you hear someone in Gundam Wing referring to an incident that occurred in Gundam 08, you will be up to par. Celebrated 35th Anniversary in 2014.
2. For Bushido: Bleach. The series starts off kickin', but the anime storyline gets a bit side tracked as it has a lot of filler stories while waiting for the next installment of the manga to be released.
3. For Ninja: Naruto and Naruto Shippuuden. Another series that started off strong, but hit a lot of "stall for time" type scenarios in conjunction to the manga release.
4. For the sake of nostalgia and first generation space mecha: MACROSS. As most fans know, Carl Macek combined The Super Dimension Fortress MACROSS and Genesis Climber MOSPEADA (Armored Genesis MOSPEADA) together to produce Robotech: The Macross Saga. However, MACROSS, in itself, is a long running series and celebrated its 30th anniversary in 2012.
Those are just the ones I can call off the top of my head.