As you may have read the other day, the FreeBSD project is now taking donations via PayPal. And if you're in a clean, roots-UNIX kind of mood, the folks at OpenBSD and NetBSD (NetBSD PayPal) would probably also appreciate your goodwill, not to mention your money, hardware and time.
If you don't have a specific project in mind, but would like to donate some of your chunk of the time-money continuum to a worthy software undertaking, a good place to start is Software in the Public Interest. They can take both general donations as well as earmark for projects they support, like Berlin, Debian, GNOME and more. (Not into GNOME? KDE could use some assistance, including money, too.)
If you like the projects funded by the boxed-distribution makers (like paying for full-time work on endeavors like KOffice), you can do more than buy the box: Mandrake has recently formed something called the Mandrake Club as a gathering place for both people and funds.
To encourage (and reward) cross-platform goodness, supporting the Mozilla project is hard to beat. (This story was posted using a 9.7 build using the wonderful Modern theme.) Source of Mozilla wisdom Mozillazine could use some help paying for the switch to a new host, and to defray ongoing costs. Another good place to cast your perls is Yet Another Foundation, which supports the somewhat scrutable development of the not-so-scrutable Perl.
More generally, consider investing some money in organizations like the Free Software Foundation, the Electronic Frontier Foundation, and the Electronic Privacy and Information Center (EPIC), all of which help battle (in court and in the marketplace of ideas) the forces who wish to monitor and otherwise exert top-down control of your computer and everything to do with your on-line life.
Remember, with all of these projects, non-monetary contributions are welcomed as well -- if you can write or correct some online documentation, create test-cases to root out weaknesses, or create some pretty graphics to smooth the user experience, you can contribute. (Long-distance pizza deliveries to developers are also generally appreciated.) Teaching a coworker, classmate, parent or friend how to set up mailfilters on a Linux box, or how to edit photos in the GIMP, is a nice way to save them money, too. Making a difference locally might also mean contributing some time, money or hardware to help run local LUG events.
Note: Many of the organizations named above are set up as 501(c) charities; if you'd like to claim any charitable contributions as tax deductions, now's the time to get the postmark, at least if it's important to you for those donations to be on the current calendar year. For a few more ideas on ways to donate geekily this year, see Jack Bryar's Newsforge column with some more links.
And a Happy New Year's!