I very much approve of this project, but I'd like to see a bit finer categorization. While its good to have everything listed, not every spell in the list make a skill strictly speaking irrelevant.
Category 1: A spell makes a skill irrelevant if and only if it provides an absolute benefit. For example, the Fly spell makes the Jump skill strictly irrelevant because Fly is simply superior to what is possible with Jump. Knock is similarly bad, since it not only unlocks locks absolutely, but opens latches, unbars doors, and bypasses wizard lock. Spider climb as written is vague enough that it may work this way, or it may be a more reasonable Category 2 or even 3 spell depending on how we interpret 'as well as a spider' and what part of the description we focus on.
Category 2: A spells makes a skill practically irrelevant if at a given level it provides a benefit that is absolutely better than what a character could recieve from ranks in skills at that level. For example, Jump when it is first acquired gives the equivalent of 10 ranks in the Jump skill, far better than the 4 ranks you could otherwise have. Glibness is an even more extreme offender. Invisibility is somewhere between this level and Category 2.
Category 3: A spell can be said to replace or enhance a skill, if the benefit it provides is equivalent to having ranks in that skill. For example, a first level spell that temporarily gave you a +4 enhancement bonus to a skill would replace or enhance the skill, but wouldn't make it irrelevant since a similar level character would have this benefit continually without spending a resource (the spell) and further characters already skilled would be likely targets of the spell since they would be the ones to naturally task with the job. Understand Device is in this category, and arguably is so weak that far from making Disable Device irrelevant, disable Device makes this spell irrelevant.
Category 4: A spell that when used creatively, can be used to replace certain applications of a skill even though that's not the spells main intention. For example, using Summon Monster 1 to find traps doesn't really make Search irrelevant, because search has many more uses than that and Summon Monster I is most likely to be only useful for finding simple traps involving pits, trip wires, and pressure plates. By the same logic, a 50 lb bag of sand and/or a 10' pole makes search irrelevant. To save you time and energy, you should just list 'Summon Monster X' as being a Category 4 replacement for every skill.
I would argue that Category 3 while definately fitting into the list of spells we would like to collect, should be viewed as a very different thing that spells in categories 1 and 2. As part of my ongoing attempt at 'perfecting' the balance in 3.0, I have for some time been trying to move spells in my campaign that are in Category 2 into Category 3, and when possible (it's not always) either increasing the level of Category 1 spells or finding a way to transform them into Category 2 or better yet Category 3 spells by changing their mechanics.