When I used to scan (about 1y+ ago), I used Irfanview's Batch Scanning feature, basically after previewing the first page (and testing various filters to see what works best with the content, to remove see through text, auto adjust contrast and colors, descreen etc) you just press Alt+S or whatever shortcut is for the Scan button and Irfanview scans the page and automatically saves it into a folder you want with the compression quality you want and auto-increments a number at the end of the filename for you.
I used 300 dpi and saving to JPG with quality 92-95, resulting in 4-10 MB files for each A4 page. Above 300 dpi, any decent OCR software won't achieve better performance so it made no sense for me to waste 3-4x the time needed when scanning at 300dpi.
Also, I don't know how it is now, but about a year ago when I still did this, Abby Fine Reader basically converted anything you shoved into it in a sort of grayscale then performed OCR, so it's pointless to scan full color a BW manual, unless you really want to.
Back then, Abby Fine Reader was the best... it could do that mixed pdf thing Halcyon mentioned, basically the background of each PDF page was the actual scanned page (picture at 100-150dpi ) and the OCR'ed text was overlayed over the picture so you could copy and paste text and it would look very nice (but resulted in larger pdf files of course)
If I remember correctly, Xerox Textbridge did a great job at actual character recognition but didn't do the layout and text formatting to my liking (i was scanning old IT magazines with columns and small pictures and the software screwed the formatting)... I also tested OmniPage Professional but for some reason didn't like it.
If you want a copy of FineReader or OmniPage for testing, PM me and I'll upload it for you somewhere.