I simply give the benefit of an item, without them actually having a physical object to hold or equip. This gives an enormous potential selection of effects to grant, with built-in ideas on how valuable they are. It also works very well if you want to avoid magical items just for fluff reasons: for the sake of the system’s expectations, you include the benefits of items, but for the sake of the setting’s expectations, you do not actually give physical items.
I then calculate the beneficiary’s assets as including the value of the item for the purposes of deciding how much loot to drop in the future. Possibly, depending on the nature of the bonus, with some kind of surcharge because the benefits do not take up a slot and cannot be removed, though in my games I tend to freely allow things to show up on “unusual” slots or for multiple effects to be put on one item, and I rarely remove items, so these are not critical concerns for me.
The custom item creation guidelines suggest that items that do not take up a body slot should cost double, which might be a good place to start when considering the value of such benefits. You may want to increase the cost from there since the benefit is greater than that of an ioun stone, which may still be stolen, or you may want it to cost less because the item isn’t worth that much to the player and the nature of the benefit doesn’t let them sell it to get something they’d like better. That’s up to you.
Also, see Complete Scoundrel’s fantastic locations, Dungeon Master’s Guide II’s places of power, Sandstorm’s touchstones, and Planar Handbook’s planar touchstones for more ideas: all of them work by visiting a special location and receiving magical benefits very similar to items. The fantastic locations and places of power even cost “effective money” the same way I am suggesting. Unfortunately, I do not believe these books provide useful pricing guidelines for custom places.