Food for the Poor has gifts starting from a fruit tree for a poor family ($10) all the way up to building a school. You get a printable card that you can give to the recipient showing what you have purchased in their name for a poor community. Most of the gifts are quite affordable, and Food for the Poor has an excellent track records for actually getting your donation to the people who need it. They have a big presence in Haiti, so this is a great way to help those people who have been through disaster after disaster this year.
Chalice is a Canadian charity that helps the less fortunate. While Food for the Poor serves the Caribbean and Latin America, Chalice serves the entire world. With gifts starting at $5 you can find something for everyone, or use these as low-calorie stocking stuffers. Gifts include things like soap, toothpaste, a stove, and many other things. Your gift is given to those who need it and your friend or loved one gets a paper or e-card describing it. You can also sponsor a child for $33/month.
Mercy Corps Gifts has 40 unique gifts, starting from $15, to help those in need. From growing pineapples to building a well, you get a printable PDF donation card to give/send to someone and a hungry child eats, a village gets clean water, a woman learns to read...
Catholic Relief Services is one of my favorite charities, because of it's great responsiveness when there is a disaster and it's stellar track record of actually getting donations to the people they serve. Through their gift program you can buy shares in a project, such as helping kids get out of gangs in Honduras, helping the victims of the cyclone in Bangladesh, providing prosthetic limbs for Sri Lankan war victims.
Catholic Relief Services Fair Trade supports the same work, but provides concrete gifts, rather than a certificate. You can buy Coffee, Chocolate or handicrafts. I can attest to the fact that their coffee and chocolate are simply the best I've ever had (well, their chocolate is the best and their coffee is as good as my next gift suggestion).
Mystic Monk Coffee is absolutely delicious. If you can, try the (limited edition) Jingle Bell Java. Yes, the web site is very slow, but the coffee is very yummy! In case you didn't know, religious orders do not get paid by the Vatican, but are independent organizations that must support themselves through their work. The "Mystic Monks" are a group of Carmelites in Wyoming who are building a new monastery and could use your help to do it.
Speaking of monks, Laser Monks provides all your ink and toner needs for printing those holiday cards and letters. Great prices, while supporting charitable works. And if you're looking for something other than ink, they also sell gift baskets and even "Benevolent Biscuits" for your dog!
The Dominican Nuns of Summit New Jersey have wonderful soaps, lotions, and other wonderful things to offer. Check them out.
If you can't decide on a particular order to support, Monastery Greetings provides a wide variety of gifts from different orders. A great "one stop" place to shop to support a wide range of good works.
I could go on and on with places to get gifts that also support charity, missions, religious, etc., but frankly it would be more than you want to read and I want to write. The above are a sampling of places I've actually used and can recommend. Fell free to let me know of others you like.