What is the best way to delete clothing from the game without borking your game?

From the Downloads folder.

I tend to use the tooltip tool along with Bodyshop and SimPE if I need to clean out large amounts of CAS items.

What is the tooltip tool?

I'm pretty sure it's this tool by CatofEvilGenius for adding tooltips to Body Shop files.

I think that the only borkage possibility in Bodyshop is if something Maxis has accidentally been given the cc star?

I believe so, although I think it can get messy and leave files behind if a piece of CC comes with many files.

Unlocked clothes with the star/bin showing.
Clothes without the star but with the bin (if that ever happens).
Some default replacement clothes (if the star/bin is showing).
Repo'd clothing (to EAxis items) can potentially also cause trouble.

Honestly a bit difficult to know at times, because there are people who can more than happily delete anything they want, and then there are people who delete one item, and suddenly they've somehow deleted some game texture files.

I prefer deleting from the Downloads folder, mainly because then I can also more easily pair meshes up with the clothes, or delete entire sets, or edit the clothes if all they need is some fixing.