Yes, that's what I'm using now. But JCrop is good for making a crop selection, and after that we have to crop it on 3rd party server, and upload a new cropped version of files back to wiki.
What I meant, was to use something in native MediaWiki Syntax, e.g. [[Image:Book_page_scan1|crop=X1,Y1,X2,Y2|thumb|this image shows only portion of page with X1, Y1 topleft corner, and X2, Y2 bottom right corner]] without having to upload new file, and just using what we already have.
You can probably do something like this with Divs and templates, but then image will be div's background, and won't behave the way regular images do.
But in the end of the day, visitors will have to load full image, to see just small part of it, and as I wanted to use it for few thousands images, on hopefully popular pages, I guess cropping and uploading new cropped images, is the way to go.
Thanks for your response.