I'd say the early supremacy wonders panopticon and master control, while dull on paper, are actually pretty good for reasons already stated earlier in thread. I don't have a strict list of best wonders, mainly because I almost never rush wonders in my game. I might aim for gene vault if I'm going purity, but man, gene vault is overrated and it is basically the new Great Library.
When I play MP, players rush that wonder and I don't know why. It's basically just a free biowell (without the health) in your city, that's it. If you need food, build some farm tiles. Since this game favours a wide approach over a tall approach, it would be better to expand your empire while you still can, rather than rush gene vault.
Ectogenesis pod is nice, but it only works on one city. This wonder is basically the new Hanging Gardens. Rushing that wonder might be a bit more worthwhile, but I prefer my own "rush" approach, which involves getting a spy agency up and running at least before turn 100 on quick. It amazes me how people put it off until they discover other people getting it, racking up intrigue in their cities to the point where they panic.
As for later wonders, it does vary a bit depending on what I prefer. Although they are generally weak, I like how they have that situational feature, so something like ansible (may have forgotten name), which gives some energy and +30 city strength would be worth having to build up defences in MP. Deep memory and promethean are both pretty good if I want free virtues immediately. Human hive is a complete waste because of surveillance web and that it'll just move the spies to other cities, not to mention that reduced intrigue accumulation rate is even better than this wonder.