It depends on the X-Cart version and Skin:
---
skin/books_and_magazines/images/custom/logo.gif
skin/common_files/images/logo.gif
skin/common_files/images/xlogo.gif
skin/common_files/modules/Gift_Certificates/images/company_logo.gif
skin/fashion_mosaic_blue/images/fashion_mosaic/company_logo.gif
skin/fashion_mosaic_green/images/fashion_mosaic/company_logo.gif
skin/fashion_mosaic_grey/images/fashion_mosaic/company_logo.gif
skin/fashion_mosaic_pink/images/fashion_mosaic/company_logo.gif
skin/ideal_comfort/images/custom/small_logo.gif
skin/vivid_dreams_aquamarine/images/vivid_dreams/logo.gif
skin/vivid_dreams_lotus/images/vivid_dreams/logo.gif
skin/vivid_dreams_violet/images/vivid_dreams/logo.gif
---
http://help.x-cart.com/index.php?title=X-Cart:Editing_Skin_Files#Replacing_X-Cart.27s_Logo