A Specific Cursed Item generally costs a fraction of the real item to craft, often around 10% (Incense of Meditation 4,900 gp, Incense of Obsession 500 gp) or 20% (+2 Sword 8,315 gp, Cursed -2 Sword 1,500 gp). An exception is if the item is especially useful, such as the Scarab of Death (80,000 gp) which could be given to an enemy to kill him in one round.
A normally functioning item with a drawback or dependent curse condition (e.g. only works in the hands of a creature with a particular alignment) should reduce the cost by around 10% to 30%, or more depending on severity. The crafting guidelines state that an item reduces in price by 10% if they require the wielder to have a certain skill, and 30% to have a certain class or alignment. You shouldn't let players pick this as a drawback while crafting, since a wizard can just create himself a staff only usable by wizards for a big discount at no penalty.
The spells remove curse and break enchantment only free a person from a cursed item, but do not turn the item into an uncursed version of itself. Since the price difference between a cursed item and its uncursed version is significant, a single spell shouldn't be enough to repair it permanently, although wish can repair items at an XP cost. A wizard with the correct item crafting feat could probably repair a cursed item by paying the difference.
Note that bestow curse does remove a curse from any item except a weapon, shield or armour, it doesn't necessarily turn the item into a properly working version. The item may have been created cursed by accident, or have broken somehow and lost its original power.
An alternative way of creating a cursed item appears in Dragon Magazine #348, October 2006, in the article "Bestowed Curses". The spell bestow curse can turn a weapon into a cursed item of its kind, so a +4 sword becomes a -4 sword. Since bestow curse is a Permanent duration spell, rather than Instantaneous, an item temporarily cursed in this manner returns to its original form when the curse is broken.