What resolution are the files you are cropping? How are you using the images? Print or screen? If print, your files should be 300dpi. For screen (web or other) they should be 72 dpi.
If they are 72dpi any increase in size due to cropping or transform will cause the images to pixelate. You can make them smaller but not larger. Start at the highest resolution you can when cropping or resizing to maintain the integrity of the data in the image.