I was attempting a new "Most Powerful Build Ever" and I got to thinking, is there anything that excludes weapons from being Wondrous Items? So: can they be?
Could I give a sword the ability to cast Mage Armor, or provide a Skill bonus?
In all these cases, the creator needs the feat Craft Magic Arms and Armor, but once that's out of the way...
Precedent exists in the form of the mattock of the titans and maul of the titans, but these are largely exceptions rather than rules, both items dating back to at least the Dungeon Master's Guide for Advanced Dungeons and Dragons, making those items' inclusion in Pathfinder pretty much a nostalgic necessity. I wouldn't count on any GM accepting these items as examples of weapons as wondrous items.
If the GM permits, the magic weapon's creator can add a dirt-cheap artificial intelligence to the weapon and, using the charts as guidelines, add whatever special abilities he desires or the GM allows to the magical intelligent weapon. However, the weapon's user must convince the weapon to use the special ability on the wielder's behalf: "Intelligent items act during their owner's turn in the initiative order."1
The feat Craft Rod (PH 92) has a broad mandate that sometimes incidentally includes weapons, like the rod of flailing. Combining rods or even adding weapon special abilities to rods that function as weapons shouldn't be a big deal.
The Magic Items section Adding New Abilities says that
Sometimes, lack of funds or time make it impossible for a magic item crafter to create the desired item from scratch. Fortunately, it is possible to enhance or build upon an existing magic item. Only time, gold, and the various prerequisites required of the new ability to be added to the magic item restrict the type of additional powers one can place.
(This text omits the GM's role in all this, but whatever.) The text then goes on to explain how a magic sword can be made into a better magic sword. Then the text continues, saying
If the item is one that occupies a specific place on a character's body, the cost of adding any additional ability to that item increases by 50%. For example, if a character adds the power to confer invisibility to her ring of protection +2, the cost of adding this ability is the same as for creating a ring of invisibility multiplied by 1.5.
That's a really high price, and puts all one's eggs in one sheath, but a generous GM may, despite the examples that seem to urge the contrary, allow a character possessing both the feats Craft Magic Arms and Armor and Craft Wondrous Item to add to his magic sword the properties of one or more wondrous items at an appropriately increased price.
1 See also the D&D 3.5 6th-level Sor/Wiz spell Nybor's psychic imprint [trans] (Magic Books of Faerun column "Nybor's Small Codex: Spells from a Former Zulkir").
RAW: No - Custom Crafted Weapons are not Wondrous Items
The rules for crafting Magic Weapons and creating Wondrous Items have completely separate pricing structures, so there would not be any overlap between the 2. There are rules for Weapon Bonuses which may help, such as Spell-Storing to cast Mage Armor if you have a friendly caster to recharge it for you.
If you did want to add wondrous properties to a weapon, it would rely purely on GM ruling, though you can use this Table to estimate the additional cost.
A good weapon is going to be with you anywhere, and with space for bonus items being at a premium, for the ability of having an extra slot for an untyped bonus, I have played using a house rule that any additional effect you add to the weapon also increase the cost by +1 bonus in additional to any other cost calculated.
The term “wondrous item” is a catchall description for anything that doesn't fall into other groups, such as weapons, staves, and so on.
So, no. You can make a wondrous item out of almost anything, but not an item intended for use as a weapon, like a sword. Oddly, you can make a magic weapon out of literally any item type (due to improvised weapon rules), so you can start with a weapon-like non-weapon item, like a shovel, handaxe, sledge, or knife, and give it both wondrous item and magic weapon upgrades (don't forget the 'slotless' cost modifier!). Unusually, for heritage content, both the mattock and maul of the titans seem to implement this combination fairly well-- the mattock's cost seems to be lacking only the size modifier, which sort of makes sense, and ends up running ~3500gp for it's limited digging ability component while the maul runs ~4K for triple damage to objects and str 18 required.
Separately, you can totally give a sword the ability to cast mage armor and grant a skill bonus. You'd just do it via the intelligent item crafting system.