Celebrim
Legend
I've just never run anything where they fit.
That could be appended to many of your entries. To me, if the monster has some strong mechanics, but weak flavor or a silly appearance, then its still a good monster I just need to reskin it. What I really dislike is monsters that could be adequately described as '8HD large monstrous humanoid'.
Howler
It's a reasonably interesting mount for packs of higher level foes when normal mounts like horses are starting to get too fragile to be creditable. You can use the Howling to harass the party before the attack, and the quills to debuff the party during the attack. I've used them before as steeds for monsters wielding mancatchers and throwing axes. It was I think a pretty good fight and provided sufficient levels of tension and fear factor, as well as displaying a good diversity of threats for me to describe and for the players to deal with.
Inevitable - Never had a chance to use them
I'm a traditionalist, and prefer modrons, but whatever.
Nightwalker - Not impressed
To me, the Nightwalker requires an extraplanar setting. I've never used one, but I can imagine situations in the near epic to epic scale where I would use.
Phantom Fungus - Dumbest Plant monster EVAR
Loved the mechanics; disliked the stock appearance. Mine look like crosses between mold and harvestmen ('daddy long legs'). They walk around on thread stalks and bend down to attack those beneath them. They have a certain Cthullan quality to them that I like, and I like how they play out in combat especially at their CR. You get this really evocative thing going like, "You feel some thing brush against your arm, almost like a strong cobweb. Suddenly there is a sharp pain in your shoulder and your blood sprays about. There is a brief outline of something pulsing red in the air near your shoulder, but it disappears again before you can really distinguish it. Roll for initiative everyone".
The great thing about 'invisible plant' is that it is really confusing especially to someone who hasn't read the 'phantom fungus' entry or memorized the SRD. I find that the secret to challenging players is to take them out of their comfort zone. With a phantom stalker, you'll often have a party lose actions to the monster because the cleric is trying to turn it, one of the other players decides to hang back in case he needs to save his skin, another player is too confused to act, and so forth. You can end up taking far more resources from them from a low CR encounter that confuses them, breaks party cohesion, and causes the player to act scared than you can from a high CR monster that provides only a straight up fight. And there is also one of the ways you can see players really develop tactically, so that over time they get more and more able to handle situations where they don't know what they are fighting (often because it is unique).
Gygaxian gaming was a lot about learning to work as a unit in situations where you didn't know what was going on and 'hit it with my sword' wasn't always an available solution. It always amazes me how much difficulty modern gamers not trained up in the old ways initially have.
Anyway, that's my many rant. I'm just saying that most of the time when I haven't used a monster, it's not because its a bad monster, but because the oppurtunity to make that monster shine just hasn't come up. The only bad monster is one that is boring mechanically either because it doesn't do anything novel, or it doesn't do anything not already done by a similar monster.