Huge differences, in some cases. In most, it's more of an "enhancement" than anything else - a re-writing by Tom Ligotti in order to drive home the story's intent or stylistic mood, without altering the original spirit.
"The Eye of the Lynx" is shockingly revised. I found the new version more coherent, unsettling, and overall enjoyable. If you've been into Ligotti for awhile, then you might know that this story used to be one of the more baffling for many readers. Thankfully, TL really did a number, breaking this tale apart, and re-building it from the ground up. In my eyes, it went from being a curiosity to a masterpiece. The Subterranean edition is worth it for this revision alone, not counting all the others.