Is this a cause you care passionately about? Has this organization touched your life or helped others you love? Is this a cause you truly believe needs your help? Sometimes we're swayed by a powerful image, or a great charity marketing campaign, but that impulsive decision may not be the one that will bring you the most happiness. So while making a gift is better than none at all, consider if there isn't a better "fit" for your generousity.
What other organizations focus on the area(s) you're most passionate about? Is there a better fit, or more direct way, for your gift to work? Websites like Charity Navigator (focused on the USA) or Charity Intelligence (Canadian but with a much smaller database) can be a big help on this front. Even a quick review of these sites may provide you with new insights about how best to direct your charity giving.
Most charities are very efficient with your donated money, but does your intended target really need your gift? How many years of operating funds does the organization have in reserve? More than just cost per dollar raised (e.g. cost of fundraising), it's important to know if you're getting real impact for every dollar donated. For example, if your charity helps students, has their cost per student been going up or going down over the last few years? And if the answer is up, have they been offering new and enhanced programs... Or are their costs going up at a rate faster than inflation?
My point is that, as I've said before, giving from your heart and from your head is important. Even if you're making a last minute donation, there is still time to do it right!