Just read Autumn's post on 1st page now. He's more paranoiac than I am and I thought I am very paranoiac. But that's a good thing.
About how I do it.
If I use adsense or same ad network that has a trackable ID or something (e.g. most have, Amazon allows you to make hundreds differetn ones for example) then makes no sense to have them on different hosts and stuff.
If they have no footprints I have them split by blackhat or whitehat (don't keep shit in the fridge nor food in the toilet). Then I have them further split by clusters so I only risk to have a few sites busted at a time. This applies to the link networks I build. Won't link from network A to anything else than a certain cluster of money sites.
Whois - I use privacy and real info mostly for great domains - as in good name - stuff like insurance.com, loanreviews.com etc. stuff where there's high value in the name. Some sites like the adsense ones I use whois privacy and real info too just because i can and is free and because they're connected anyway.
Then sites that i need to look without having a connection to eachother I may use fake whois info. And here I include money sites that may make good money. I just prefer the privacy over anything else bc without it you're screwed. In the event a registrar would ask me why the different whois details, I'd reply that I am managing sites for multiple clients and I expect that to shut them up. Never had anybody inquire though.
Hosting is also clustered similarly. What dictates how i cluster is the footprints I can't avoid. So all adsense sites are on same host bc makes no sense otherwise. Whitehat sites on 2nd host, 3rd host, 4th, etc. depending on how many clusters u need. Same with blackhat sites but always separated from whitehat ones.
It is a bit of a hassle to cluster sites not because it is hard to do it but because it is hard to bend ur mind around a bunch of clusters each with its own plan, links, content, accounts, etc. You you can't make any mistakes to leave connections or traces between them because if you do, you just potentially screwed the privacy of an entire cluster or several clusters. Happily while I have many domains, I don't have that many live sites anymore. Though I guess will have in a while.
Most footprints u leave however are much simpler and dumber ones if you don't understand the link algorithms and some important stuff. Link profiles can tell a lot about 2 sites. They may not be obvious enough in a court of law for example but they are obvious enough for somebody at google to say "these two sites look too similar in the link graph to be a coincidence". You want to avoid that. Then if somebody digs deep you have the HTML, CSS, JS files which can have indicators they were developed by same person. Trust me you potentially can tell if 2 CSS files hae a good chance to be coded by same coder. There are a lot of things that are footprints and a good doxer can figure them out. But there's a balance of how much paranoiac you want to be and how relaxed. Neither of the extremes is good.
About hosting all on same IP and what Matt said about it not being a problem bc most people use shared hosts and stuff. Well, if you have 10 BH sites, 10 WH sites on an IP with 1000 other sites from tens of registrars and stuff then yeah that's all cool. But if you buy a dedicated IP/VPS/server and have 100 BH sites that seem to follow the same pattern then you can bet all are going down when found. And it has happened and even Matt in a video said something along these lines.
The key with blackhat is not to be a badass and look like a badass but be a badass and look like the most innocent child born on this earth, with puppy eyes and soft voice. Proper blackhat is not when you figure a hole in google's algo but when automated stuff that takes you 10min to do looks like real stuff done by 10 people in a year worth of work. Not when sites you make trick google's algos but when they trick any bot and human and anybody would see them as useful and nice sites.