I’m using the phase vocoder and the arpeggio sampler a lot for live sampling in a few projects but I notice that the organelle seems to cut out a lot of the low frequencies. Just wondering if this is because of limitations of Pd or the organelle itself? Essentially, is there a way to get some of the low end I know the organelle can produce when using the sampler based patches?
I know it has been a long time since you posted this, but if you still didnt find a solution, you could try adding an extra sub(sine) oscillator to the sound you are working on. So you have the main osc, a saw maybe, and then a sine sub osc to add some fatness. This gives it a bit more punch, imo.
Another thing is oversampling, but this is a bit tough wit Organelle since we have limited ressources. But oversampling will also make sound sources sound more “fat”. Not the technical term of it, but you know what i mean 
Example of oversampling can be found in Pure Data 3. Audio examples/J07.oversampling.
besides that type of oversampling you can also try maybe adding a the bob~ filter and use bob~s oversampling. But if I remember correct bob~'s oversampling is pretty heavy on Organelle.