I was messing around with particle emitters for a bit and noticed something that would be quite irritating if it were to come up in a game at all. I noticed that even if a BillboardGui has AlwaysOnTop set to false that the particles will not be visible where the BillboardGui is. Particles will only be visible when in front of a part and without the BillboardGui in the background. Particles should probably not be doing this as what is seen below would be quite awkward in a game setting.
The part at the top is the part that the ParticleEmitter is placed within, the block at the bottom is the baseplate and the part that the BillboardGui is in is in the distance.