I think I'm right in saying you can only hook up a different shader to a particle effect, in which case you could in theory construct the majority of the ship as a mesh for the particle system to achieve that. The main ship mesh would just be an untextured minute black cube.

The particles use a different shader to the ships.  It's why it allows transparency.  you would need to write a new ship shader that uses another texture.  Right now on all the textures, every chanel is being use (RGBA)  Alpha has different uses in our game.

So that being said. The first place to start is writing a new ship shader.

If you are talking about effects such as transparent force fields and such (I assume that's what you mean by "permanent billboard effects") then yes, you can do that. It is also possible to use this for permanent 2D geometry simulation (something simmilar to what the old EvE ships used to employ with those complex girders).

You do it through the particle system - basically you create a flair point with a custom made texture which has its alpha adjusted to produce the transparency effect. Make the lifetime infinite, and the particle count set to 1 and you should be good to go. I used this method succesfully to create hangar forcefields.

Other than this, I don't think you can do partial mesh transparency, as that would require the model to use a completely different shader than what is currently available. Also, using TGA files would probably produce unwanted results (if it would work at all, which I doubt) because you'd lose MIP maps.

It *should* be possible to use the above particle method for 3D transparency effects, like bubble domes or canopies, by using an actual piece of geometry and simply adjusting its transparency with an instant color oscillator (it has alpha control as well) modifier - in case the normal transparency control in the color picker doesn't work on mesh particles, haven't tried it that way yet.

No it isn't. Billboard particles are a very efficient way of doing this. You are dealing with a single infinite life particle, and if you use low-res textures you should not have any problems. Sins engine is very good with particle rendering - one explosion contains enough particles to cover for a whole fleet worth of billboard instances.

For example, my ships frequently use such instances to render floodlight effects. Usually there are several of those per ship and I have yet to notice any slowdown due to using particles in such a way.

Like ManSh00ter said, each billboard particle is ONE particle.  Size doesn't matter here.  For each effect, only ONE particle needs to be processed and rendered.  A standard explosion has more particles than a fleet's worth of these, and the resources required for a fleet's particles will be almost non-existent compared to the resources required for the polygons/textures.

I under tristans point about the render engine issues with particles, it is an alpha clipping problem which honestly is not very nice regardless of how fast your video card is (especially the more alpha sorts that are needed.

what I am specifically looking for is a way to create billboards that have organic tendrils on them, with at most a capitalship having 10-20 of these billboards arranged in a halo around it. The stated method worked acceptably in HW2 (except for alpha clip issues when particles overlapped one another) thanks for point out that I can use flairs. the only specific issue I may run into is that I need the position and rotation fixed to the mesh get the necessary effect (using parallel in the particle forge looks like it will do this)

the alpha clipping is when a texture/shader withalpha is displayed, at a certian point the graphics engine (any graphics engine will do this at some point) could care less what is behind something else and either defaults to a solid color or ignores any additional particles. The important part here is how efficient sins particle sorting engine is for performance, saying that there is no performance impact is just saying that there is no performance impact that you can readily notice (have you tried checking the frame rate hit in the debug .exe for large particle counts, it is really high)