Sometimes I just manually crop out (using freehand selection tool) a few leaf clusters, and piece copies of the clusters (rotated mirrored etc) together to make a branch.
For textures made from a single photo, (like the pine branch above) I have the same problems you mention. But I start with a high resolution photo so the pixels will be small enough to get a clean edge. Then I decrease the image to 256 colors and change the blue-sky or white background colors to black using (edit pallete) . There is often a bluish/whitish border around the leaves still, so I finish by darkening the whole image. That usually gets rid of the light colored ring. Finally I resize to 256x256 which further blurs out any lingering color problems.
For textures made from a single photo, (like the pine branch above) I have the same problems you mention. But I start with a high resolution photo so the pixels will be small enough to get a clean edge. Then I decrease the image to 256 colors and change the blue-sky or white background colors to black using (edit pallete) . There is often a bluish/whitish border around the leaves still, so I finish by darkening the whole image. That usually gets rid of the light colored ring. Finally I resize to 256x256 which further blurs out any lingering color problems.