I have a player in my group that likes tanglefoot bags and thunderstones and such so much that he asked me to create an "alchemist" subclass for his character, which I did using a version of the one created in Feudal Lords. One of the things he loves about playing his alchemist/herbalist/sorcerer is that he can't just whip them up whenever he feels like it. He has to find the materials, and successfully craft them. He likes the process, and since I make him work for every one he makes, he is constantly nagging the party to use them wisely. It makes for great roleplaying and in our world they have pretty limited use anyway. But they are very useful for a low level party that gets caught with their pants down. Their 1st level party's first encounter was a chance encounter with a dire wolf out in the woods. A couple of tanglefoot bags (these were given to the party by the character's mentor, he wasn't able to make them yet) bought them enough time to get outta Dodge. My players aren't a "kill everything that moves" kinda bunch, so Tanglefoot Bags are great for evasive maneuvers too. I could totally see though how they could get abused by players with more of a videogame mindset. Of course, just about everything in D&D is abusable by a videogame mindset by either the players or the DM.
As a DM, I feel like my job is to tell a great story that allows the players to be the hero how they want to be the hero. If I have a player who wants to play a alchemist/herbalist/sorcerer who's main job is to create the materials needed by the party for their jobs, then I find a way to make it happen. I was worried about tanglefoot bags being a little too plentiful, so I just make the process of creating them a little bit laborious and a little bit time-consuming in game, so that he doesn't have his character just sit there mass producing them during downtime. I treat alchemy just like magic in my world; something rare and powerful and wonderful. If I don't treat things as mundane in my world, my hope is that my players will also perceive those things as rare and powerful and unique. That's why I don't have Magic-Marts or Bob's House of Potions in my worlds. Finding the crafters of such things are a mini-quest in and of themselves, which keeps availability to manageable levels and better represents the kind of world my players want to play in.
Just as an example, the party was seeking out someone that could help them discover their purpose for being somehow teleported into a glade in a forest together. They stumbled upon a Loremaster who had envisioned meeting "4 strangers who were friends by circumstance" that he knew he was supposed to aid. In addition to being a Loremaster, he is also an alchemist and has taken Michael's character under his wing to teach him alchemy. Michael's first task was to learn how to make Tanglefoot Bags. The ingredients are rare, and can only be found in the desolated part of a lush forest called "The Dead Wood". The Dead Wood is a dangerous place, a place destroyed by negative magic gone bad and has twisted and distorted everything in this part of the forest. So, in order to get the materials to create Tanglefoot Bags, the party is going to accompany Michael into the Dead Wood to procure the materials. It's a mini-quest in and of itself that serves me several purposes as a DM, and also paints the picture that creating some alchemical substances are somewhat dangerous. The party somehow found that a lot more fun and interesting than just plunking down a bag of gold at Alices' Alchemy Barn.
So I guess my long-winded opinion would be; don't ban them, just make them a bit of a pain to acquire. This will keep quantities manageable, paint a more tangible world for your players, and give you a couple more hooks for small side adventures. I use this approach with everything magical or holy in my worlds and the players really seem to like it. Mechanically speaking, it's not really different. I don't charge more for the items or nerf the items. I just make them a little harder to obtain, and everything else seems to fall right into place.
