Some of the Nephilim are actually fairly good cards that see some play in some Commander decks. It is a shame that they were not Legendary Creatures, as a couple of them could have been very playable Commanders. Magic the Gathering head designer Mark Rosewater - better known as MaRo - wished they had made them Legendary in the first place.
So, we have these 5 Nephilim. Let's take a look at each of them and their overall playability, even as unofficial Commanders.
The best sort of deck for a card like this would be one like a Maze's End build with Child of Alara as its Commander. Such a ramp deck that has Maze's End for its win condition would be happy to have a card like this who could make a whole bunch of tokens to either hold down the fort or serve as an alternate win condition. For those unfamiliar with Maze's End, its primary purpose is to pull Guildgates out of the deck. When it and all 10 gates are on the field, you win the game. Building up an army of Sand creature tokens while working to accomplish this goal is definitely good.
Unofficial Dune-Brood Nephilim Commander decks would obviously focus on getting a lot of lands into play quickly. Sadly, since you're missing a color, the Maze's End plan won't work. However, there are plenty of ways to still get a lot of lands into play quickly. Key cards in this strategy would include The Gitrog Monster (himself a powerful Commander) and Splendid Reclamation. Having to sacrifice lands to the Monster is fine since you can just get them back into play with Splendid Reclamation. It's an interesting deck concept, although Gitrog Monster himself can do this a bit more consistently. Still, having access to Red and White allows for a broader spectrum of ways you can win the game.
Glint-Eye's best deck in Commander is easily Rainbow Creatures, a deck led by Progenitus that uses all 10 of the Shadowmoor/Eventide Lieges for pumping its creatures, as well as all 5 of the Kamigawa block Myojin, and all 5 Nephilim. It also plays all 5 New Phyrexia Praetors and all 5 of the major Theros Gods. The idea that Glint-Eye could get very, very big and draw you a lot of cards is pretty awesome.
If you're looking for ideas on how to build an unofficial Glint-Eye Nephilim Commander deck, EDHREC has a few lists that you can draw from.
"Whenever a player plays an instant or sorcery spell, if Ink-Treader Nephilim is the only target of that spell, copy the spell for each other creature that spell could target. Each copy targets a different one of those creatures."
While that's a fascinating ability, how exactly is it used? Besides being played in Rainbow Creatures, Ink-Treader has found a home in Chaos-based Karona, False God decks. These decks play very few creatures and focus around making the board-state as crazy out of control as possible. What Ink-Treader does in a deck like that is make it so that it's basically impossible to remove without destroying every other creature on the board. It's a tricky card, which would be a lot better were it a Legendary Creature that you could build around.
Unofficially, you could build a pretty fun Ink-Treader Nephilim Commander deck. If you're looking for ideas, EDHREC has quite a few suggestions for you.
What Yore-Tiller allows you to do is bring a Dragon back into play tapped and attacking straight from the graveyard. Yore-Tiller has to attack to activate this effect, but does not need to deal combat damage. More often than not, it will probably be blocked and killed but whatever is brought in with that effect is likely going to deal a lot of damage, especially if it's a Balefire Dragon or Hellkite Tyrant, or the like. Yore-Tiller has also seen some play in Sliver decks, to help bring back key Slivers from the graveyard.
Were Yore-Tiller Nephilim a Legendary Creature, it would be the best of the 5 as a Commander, as well, allowing for a very solid Reanimator deck, only lacking Green. Here are some suggestions on how to build an unofficial Yore-Tiller Commander deck.
Overall, the 5 Nephilim are all fascinating creatures that had they made as Legendary Creatures would have provided 5 very interesting Commander options. And as we've seen, people have used them as Commanders, despite not actually being Legendary.
Even with some proper 4-color Commanders available now, the Nephilim remain fascinating curiosities, all of which see some amount of play in Commander.
And, of course, all 5 are playable in the rarely played Prismatic Magic Online format... not that anyone will ever care about that format again.