I believe that both XSane and Simple Scan can do this. In Simple Scan,
Each page you scan is added to the end
of your document. To start a new
document select Document ▸ New.
Individual pages can be deleted by right clicking a page or pressing the
Delete key.
In my experience Simple Scan is easier to use in general, but I have not used it for this purpose specifically.
If your main goal is to produce a single pdf at the end, then you can always scan each page and save each page separately with a filenames such as document-page-01.pdf (note that I used 01, if you have more than 9 pages, this is important in order to ensure proper sorting of the pages in the final document) then you can use ImageMagick's convert command to easily merge them into one document:
convert /path/to/document-page-*.pdf combined-document.pdf
ImageMagick can be easily installed on every major Linux distribution. Another tool that will yield similar results is pdftk which, according to the website, uses the following syntax to merge files:
pdftk /path/to/document-page*.pdf cat output combined-document.pdf
I've always used convert since it is a great swiss-army-knife-type tool for image files, but I'm told that pdftk is often much faster and produces better pdfs using the default settings.
This is often nice for when you already have a long pdf and want to append pages to it.