I've found the problem. Previous versions of Limewire didn't give a crap how many files were in your download directory, so long as you weren't sharing it.

4.9 does. And there were over 40,000 files in it (though only 499 shared).

Moving some of them and cutting it down to 20,000 produced a performance improvement. Moving more of them produced a bigger improvement.

Limewire's memory use shouldn't even be scaling with the size of a disk directory IMO -- that's the whole point of something being a disk directory, so that only some of it needs be referenced in memory at a time.

Limewire's CPU use certainly shouldn't be scaling with the size of a disk directory. It should only scale with actual activity -- user input, active uploads, active downloads, and active peer connections should contribute to CPU use, and nothing but these. Yet downloads "awaiting sources" still seem to contribute, and in 4.9 even unshared files sitting in the download destination folder seem to contribute.