Owning a prophet 12 as my main workhorse synth for a few years has made my synth-programming style eat mod slots for breakfast.
I often have slots do conditional changes, for example when the slider is up, mod wheel will do different things than when it is at zero. Basically tons of mod slots affecting mod slots. Note number and velocity affecting envelope shape and characteristics, fx parameters, random modulation to change each note slightly, a bit like the vintage knob, but also in less subtle ways etc.
Often i end up with a '4-vector quadrant' like setup, where there's 4 sounds or variations of a patch, 1.MW down+SLdown, 2.MWup+SLdown,3.MWdown+SLup,4.MWup+SLup. And you can of course morph between them. (and then there's the actual patch morph
I also really like to use modulation to the delay and reverb algorythms and envelope changes to trigger 'Freeze'-like effects from the slider.
I don't think i've made many patches that don't use all mod slots (well minus the ones where i run into aforementioned problem) And it's really frustrating when you end up with a great sound, but can't use it unless you give up one mod slot (making me having to redo the whole patch several times in my head to determine what routing is least vital to the sound)