This is a question that is entirely dependent upon the group of people playing, buyin/rebuy size. game size, personality traits, etc.
When my group is a single table, or 10 people total or less (two tables of 5), we just do winner take all. We run a $20 buyin / $10 rebuy game. We buy pizza for the group from the pot. After all is said and done we may only have $100 or $120 in the pot on smaller nights, so winner take all makes sense, especially if the game is wrapping up by 10:30pm or so.
For larger games, we do it a little different. I have 18 people registered for this Friday's game, so the bigger pot warrants more payouts. After rebuys, pizza cost, etc., we'll probably have $350 - $400 in the pot and we'll do payouts for 1st, 2nd, 3rd. We don't stick to a strict percentage, instead, we just go with easy numbers that make sense. If, for example, we have $360 in the pot, we would probably just do something like $200-$100-$60, or $200-$120-$40.
Once rebuys end, and pizza has been ordered, I announce the pot size and we just vote on a payout structure. It usually doesn't take more than a minute or so... everyone is usually pretty loose on booze at that point, and they just want to play. I'll throw out a structure and just get a lot of, "sure - that's great - just friggin' deal!" responses.
At the final table, we also let players decide payouts. One night we had our final table going to 2am with headsup play... the two players were tired and wanted to go home, so they just agreed to chop the top two payouts. As host, I had no issue with this. But, we're a low-key/easy-going group. In other groups, I could see defining payout structures being a more serious/onerous affair - especially in games with much higher buyins.