Which one am I thinking of then?
Aaaanyway, it's something that you can do yourself for the most part. The major offenders are the items that are brought onto the map, especially by traders. Sooner or later they'll bring every combination of animal, leather, meat, and clothing onto your site, and they're not removed fully from memory when the items leave.
My raw-fu is a little weak these days, but I think the following would make for a minimum of typing and fewer things appearing:
Leather: change the 'tan a hide' reaction to use a specific material instead of the material of the animal it came from. For this I would use the leather of a dummy creature (ie. one that doesn't exist and has only the bare minimum of raws for the tanning reaction to be able to call its leather. I used this once for alchemical substances I didn't want turning up in preference lists). You'll end up with every creature in the game producing the same type of leather, but you don't need to go through every creature and make changes.
Clothes: remove clothing from the raws until you have one item each for the head, upper body, lower body, feet, and hands. For the upper body I'd recommend keeping cloaks as well as whatever you choose, because they cover a whole bunch of areas beyond the upper body they're 'attached' to.
Crafts: trash these.
Prepared fly brains and god knows what else: remove [MEAT] from any material you don't want the traders bringing as food. This will mean a lot of gizzards and sweetbreads going to waste, but animals generally produce enough muscle for a fortress to live on. At least, I always seem to end up swimming in offal roasts after a while. With a search and replace, you could maybe make the organ meats edible only when cooked, which will allow you to use them but stop traders from turning up with them.
Armour: there are fewer of these than there are types of clothing, but you may wish to remove anything you don't use in your own uniforms.
Stone and gems: this is more of a hit to the vanilla-ness of the game, but you can get rid of most gem types and a lot of the small clusters of stone that have no particular use or unusual colour.
Other food and food-like items: You can remove redundant plants (two of the berry species spring to mind). I don't think there's any way of stopping traders from bringing barrels of blood. There are probably more varieties of fish than you care about, and on a related note there are probably a lot of vermin you don't care about either.