As regards beams, you may be asking the wrong question. Been a time since I consulted the reference bible and so on, so I don't know what technobabble is regarded as "canon" and thus can't be contradicted or everyone will run around screaming and tear their hear out- but ingame they're instantaneous, and there's ways to run with that physically. Think of it this way: we've got the whole subspace thing going, so alternate dimensions that can be used to flaunt the laws of space and time are already considered a reality in the game. The Shivans are a race that practically lives in one of these reality-warping alternate dimensions, and certainly are highly skilled at making use of them. They invented beam weapons.
So why couldn't the beam weapons be, instead of a traveling spray of coherent energy-of-some-sort, a one-dimensional rip in three-dimensional space that appears simultaneously at every point along its path, with one termination at the point of the beam projector (really some kind of Fancy Science Thingy along the lines of whatever makes those big shiny subspace "warps" appear in front of ships when they wanna bugger off- they even say in one of the briefs that nobody really gets how beams are supposed to work), and the other either located at a computer- selected point inside the target, or at some ridiculous distance away (or infinity)? The sudden temporary removal of even a fairly small slice of the universe would be pretty catastrophic all down the line- the glows surrounding beams themselves would be the result of trillions upon trillions of tiny nuclear explosions occurring as the (relatively) miniscule number of free-floating hydrogen atoms you get even in deep space met an infinitely thin line of condensed annihilation- and wouldn't affect spacetime disturbances like shields so much as more tangible things like the component atoms of all those parts of spaceships pertinent to keeping air and burning fuel in and the vacuum of space out. Why shields wouldn't take damage from a very small part of the ship they contain and the space around them going Hiroshima I'm not prepared to bull**** my way through, but there you go. You couldn't, say, slice through a planet or even a fighter with it, it's not that kind of weapon, but simply by making life very unpleasant along a single moving line all the way through to the other side you'd bypass any armor that ever existed or ever will and utterly mutilate anything with important internal machinery vulnerable to nuclear fission.
Also, while I'm extremely rusty on my particle physics last I remembered plasma was more or less containable by a strong magnetic field, and in fact could be magnetically polarized itself (this from playing around with the theory regarding Tokamaks). So presumably, were one to run a fairly coherent cloud of plasma through a ridiculously powerful electromagnet (or, better yet, a few of them), it would become highly magnetized in and of itself, trapping itself in its own field same way as a ball of magnetized iron filings will stick together without external interference, and would remain coherent until the field dissipated. This would have the added effect of allowing you to propel the thing using extant and relatively efficient technologies without having to touch the ****er. So there's your plasma ball right there- they still couldn't travel as slowly or be as coherent as they seem ingame, perhaps, but given sufficient power levels (which FreeSpace seems fond of exhibiting to the extreme), they'd be feasible at least.
