OK , here are some of my experiences (as being an orchid breeder).
In most cases I have noticed that it does not make too much of a difference if you use one parent as a pod or as a pollen parent. I usually do it both ways, so I have double the chance of getting a seedpod.
The only time it would make a difference if it involves genes that are in the plasma of a cell. They only get transmited through the next generation in the egg cell, so when you would use that as a podparent. Now you have to remember that more than 99% of the DNA is in the nucleus. There is only a small percentage of DNA that gets inherited through the plasma (mitochondrial or chloroplastic DNA).
Now I know with breeding Paph's people have told me if you make a brachy x multifloral cross. It is better to use the brachy as the pod parent. If you do it that way you getter better shaped flowers. I don't know if this is true or not.
Also I have heard that if you use Paph. delenatii, it is better to use it as the pollen parent. Paph. delenatii has dominant genes, that are probably in the mitochondrial DNA that makes the colors lighter; it washes them out, so if you use delenatii as the podparent the offspring will be lighter in color than when you use it as the pollen parent. That is why when you make Paph. Magic Lantern it is better to use Paph. micranthum as the Pod parent; you get darker flowers that way.
Also out of own experience we have noticed when we make Phrag. Jaosn Fischer it is better to use Phrag. besseae as the Pod parent. The flowers tend to be better shaped, than if you use Phrag. M. D. Clements as the pod parent.
when it comes to yellow pigments, I have also heard that some of them get inherited through the mitochondrial DNA, so if you are breeding for yellow colors, it is better to use the yellow flower as the Pod parent. I do not know if this applies when using Phrag. besseae flavum, or Paph. armeniacum.
Another thing you have to keep in mind when breeding two flowers that are different in size (think like a Phrag. fischeri or Phrag. schlimii versus a Phrag. caudatum), is that you get a better seedset, when you use the smaller flower as the podparent. This is because the pollen tubes of the smaller flower won't be able to grow as long as the pollen of the larger flower, so if you pollinate a Phrag caudatum with a Phrag. schlimii only the top part of the ovules will get pollinated.
Well I can write whole epics about this topic, but I have to get back to work.....
Robert