1 VA with Beam Overload 1 in a Peregrine with 1 Mark XI purple dual beam array and 1 Mark XI Hargh'Peng = good probe duty. Add a science player to the mix and you got a tiny fleet of distractions for the mother ship.
With the fighter why not use a cannon? If you're using a Beam Weapon Then might I suggest the Delta Flyer?
I've done a few RA's in the Fighter (yeah I'm THAT GUY) and it does make for an interresting challenge. Though for the standard shuttles, I'm not too sure what they would be good for other than getting the Delta Flyer.
The standard Type 8 Shuttle is pretty useless, but you get it for free. The Danube Class Runabout has superior shield and hull strength and has a native Tractor Beam I ability built in. If you are willing to lay down the 30k or so EC to buy it, then you're better off with the Danube.
Because when you have played all there is, earned your 100 Million EC, got bored with the Accolade hunt, maxed a couple of characters (Fed & Klink), capped FDC, opened up all the R&D ..... there is not much left to do but buy the shuttle to give you 10min of sad sad STO joy
a Shuttle Vs. Shuttle PvP queue would be nice. I usually take on out to do my anomaly grind in low level exploration sections. It's also great fun to fly your Delta Flyer into an RA and try to recreate the scene from Voyager where it blows up