Autobombs are gloriously wonderful -- build (a half dozen) space port thingies right outside a wormhole and spew exploding death into it (or set the waypoint to several sectors out and wipe clean a whole swath of the galaxy), or bring in the mobile builder thingies. It'll strip entire systems of everything but the guard posts without your actual fleet having to budge. (Maws are actually pretty great -- full pop can functionally erase huge swaths of smaller stuff, and still soak up a nice chunk of damage for your own doodlings.
Any of the neinzul stuff -- except, perhaps, the shrikes -- are absolutely amazing in practice. Railpods are obvious, but I'm particularly fond of the weasels (ridiculously tanky for their cost), fireflies, and... one of the other ones I'm forgetting the name of. It's like fireflies, but one of the two makes things explode and the other does percentile damage. Both great. And the... whatever they are. The reclaiming suiciders. They're great -- spam them everywhere, never build a fleet ship beyond 'em, still get full cap everything.
Tackle drone launchers are absolutely beautiful. Complete neutering of almost every non-starship with just a handful. Full pop of them can hold off several hundred little dudes easily, if they're not immune to tractors.
Really, almost every single bonus ship -- barring the boring stuff like MRLSes, or the non-suicide really low HP stuff (and sometimes even then -- the autocannons or whatever they are are actually superbly brutal if you can keep their numbers up [and that's what mobile docks are for].) -- is objectively wonderful, to the extent it's not really a question of "better" or "worse" but rather "What do I feel like shoving up the AI's electrocloaca today?"