You can use any photo editing software to do a watermark. You don't need specialized software to do it.
I have Photoshop CS4 and PaintShop Pro x4 and do my watermarking with them.
What I have done is created a watermark and logo in 900x600 and 600x900 and saved them as a png. I edit my photo and save a hi-res copy. Then I resize it to 900x600 or 600x900 for web use. I open my watermark and copy it, and paste it as a new layer. You can mess with the opacity and make it lighter then the image so it doesn't interfere with the photo.
Also, Paint Shop Pro and Photoshop have a tool for watermarking.
An example is attached, which is jpeg so it has a black background, but a png will keep the background transparent. I just threw this together in a minute so don't use the not centered as an example lol