I adore Pixedit; have been using it for years. It will indeed crop the borders, but (unless there's a newer, updated version) won't do so automatically.
Quickest crop is using the selection tool (the one that's on by default when you open a document) to surround the content you want to keep, and then shift-delete to remove everything outside of it.
You can also use the auto-deskew, either page-by-page or for a whole document. However, it sometimes picks an odd horizontal point and skews the whole page badly; you can Undo this (on each page individually, rather than the whole set at once) and manually deskew the page instead.
Filtering to remove objects smaller than 3 pixels will get rid of most speckles for up-to-300dpi scans. When re-setting the filter numbers, watch your I's and .'s; when it starts to remove dots from letters & punctuation, it's set too high.
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