Henry said:I do know of some examples.
The obvious ones:
Invisibility vs. the hide skill
Charm Person vs. Diplomacy
'Disguise Self vs. Disguise
Feather fall vs. the fall reduction aspect of tumble
Spider Climb vs. Climb
Even in these examples, however, they only overshadow the skills in a transitive way, because they aren't permanent solutions to the kinds of quandries that skills can solve. A person Charmed will be likely hostile if he discovers he's been charmed, unlike winning them over with diplomacy, tumble fixes more than just falls, disguises don't detect as magical, invisibility wears off unlike a skillful hider, etc.
This Iron Heros Design Diary actually has a complete chart of what skills are "overshadowed" by what spells:
http://www.montecook.com/cgi-bin/page.cgi?designdiary_mmearls_16