I don't think there is a real way of temporarily suppressing the magic in a magic item except with dispel magic which only lasts 1d4 rounds after a succesful caster level check.
I can however give you some alternatives to meet the purposes you listed.
Hiding magic aura
The spell level 1 Magic Aura allows you to hide the aura of a magic item from Detect Magic for 1 day/ caster level. The downside is that a will save is allowed to overcome it. However, the level 4 spell Greater Magic Aura will NOT allow a will save to overcome it. Greater Magic Aura only exists in pathfinder, Magic Aura also exists in 3.5.
As Ols pointed out, a thin sheet of lead also blocks detect magic. Thus creating a small box with a build-in sheet of lead, and keeping the evil/cursed items in this box would thwart detect magic.
Handling cursed items
Remove Curse is your friend. It doesn't remove the curse but it does allow you to get rid of the cursed items. Usually cursed items like to stick around so you can fully enjoy their penalties.
Remove curse does not remove the curse from a cursed shield, weapon, or suit of armor, although a successful caster level check enables the creature afflicted with any such cursed item to remove and get rid of it.
Safely transfer evil magic items.
I would suggest simply smashing the evil magic items so you don't have to transfer it to begin with. You could even do that while you're fighting the bad guy wielding it. (Sunder)
If you do have to move a evil magic item (maybe you can't destroy it, like an evil artifact), I suggest at least putting it in a Bag of Holding so it's in another dimension. Things tend hurt you less when they're in another dimension.