This is what I am currently using for effects.

1 - First I run into an equalizer 

2 - Then I split the signal into 4 parallel signals with a rolls mixer.

3 - I run one of the parallel lines into the Line6 bass pod where I model an acoustic 360 with a rat or big muff distortion pedal. I use this to get a retro growlly distorted sound. Or I also model an Ampeg fliptop with the Rat Distortion pedal. And I also Model an old Marshall amp. With the bass pod I can get a wide range of clean or dirty sounds and various effects and model different amps and speaker cabinets.

4 - The second parallel signal goes into a MXR bass di+. I use this pedal to get a clean modern sound. It also has a distortion button that can give a moderate to extreme amount of modern distortion.

5 - The third parallel signal goes into a Marshall Guv'nor. This gives me an old 60s marshall stack sound. This can go from a small amount of distortion to an over the top marshall sound. This effect can give you a the classic Jack Bruce Cream tone.

6 - The fourth parallel signal goes into a Tech21 VT Bass pedal. With this effect I get a slightly dirty Ampeg SVT bass amp sound with a tube like growl.

7 - Then I remix the 4 signals back together and run it into a bass amp, or pa, or studio mixer. Because the signals are parallel I can mix clean and overdriven sounds together and still get effect and a sound that punches through the mix.

Sound byte with a 5 string fenderbird   Sound byte 1

Sound bytes for each effect isolated using a 5 string jazz bass. 

MXR Bass DI+    Marshall Guvnor   VT Bass   Bass Pod 1  Bass Pod 2    Bass Pod 3

Schematic diagram of my effects.

Here are 2 pedals I am considering adding to my effects board.