Pretty much any of the child-centred stuff like growth vats or kid clothes or etc. I guess I just don't like kids very much

The entire growth vats system

Nature shrines. You're leaving psylinks on the table if you do.

I haven't really tried the gene editing stuff. I'm sure there's some ways to make superhumans with it but it seems like a huge pain to set it all up.

I have legitimately never used the orbital laser thing. Every time I get one I hold onto it for 'when the situation is really dire' but never end up using it.

Is it possible to sell your colony? Outside the archonexus plotline, I mean? I've done it once (the plotline, I mean), and that was enough. With my conservative play style, it's too tedious to do it all three times. If we're including endings, I've yet to host the High Stellarch.

As far as stuff, I've never used growth vats since I prefer quality colonists over quantity. For same reason, I've never used any of the slave stuff or most of the royalty clothing (robes, vests, crowns, etc.). I've not yet tried many of items from Anomaly, like the serums. The downsides just seem too large (which I understand is to offset the benefits, but still...).