From my own experience, the quality of the scan and the damage to the book are proportional to each other.
That means, the better you want the scan to be, the more damage the book has to suffer.
I only have experience scanning tanks, but I know a good deal of folks who have scanned doujinshi too.
First off, you need a decent scanner. I mean it - maybe it's my OCD but I couldn't get acceptable scans with my old one, so I bought one a certain Anonymous Scanner recommended to me.
About the scans itself - there are roughly two basic methods how to deal with that.
Either dismantling the book or putting the book flat on the scanner without taking it apart.
Putting the book on the scanner as is can give okay scans if you're willing to press down the book hard enough to make gutter shadow disappear (that's the part of the book between the pages, on a scan that will look dark). That means damaging the spine, essentially.
Doujinshi have fewer pages, so damage to the spine (if there is any - I never had a doujinshi in my hands) might be negligible.
The other method, taking it apart, will result in greater quality scans overall. It basically comes down to your preferences in quality compared to damage to the book. Not saying un-debinded books can't give you good scans, but there is always a trade-off.
If you want to debind, don't TEAR off the pages from the spine! I know some people who do that, and it may have worked in their case, but it produces spine rips and may even rip the pages in half.
Happened to me once... not fun. I prefer the hairdryer method, basically you melt the glue in the spine until the pages come off. It's really easy, and no damage done to the pages except the obvious debinding of the book.
Oh yeah, and you might want to use black paper and put it behind the page you scan so you avoid bleedthrough (that means you can see the other side of the page shimmering through, which is sometimes hard to remove in postprocessing - and it looks kinda awful)
The guide to post-scan processing Shanko gave you should point you in the right direction.
Here, have another two:
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http://www.ruinevil.com/rawr/editguide/1.html[
senbonzakura.kageyoshi.net]
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