PS - Flattening layers

I've read a few times that some of you flatten your layers in photoshop before saving your lo. Something about drop shadows? I've noticed mine do shift a bit when I save, but never really paid attention to exactly what happens. Do you flatten before you save as a jpg when you're saving the 12x12 for printing, just the ones you save for posting, or both? Or none? Does it effect/affect(I'm too tired right now to think about which one it is!) the filesize?
Ugh, I don't know, just was wondering about this, if it's something I should be doing that will help the quality. If you do flatten, would you tell me why?

Hiya!

I use an action to do my resizing for web. But the first thing it does is flatten it. I also merge layers before I do my custom drop shadows cuz I think it makes PS a lil fasty when saving.

I think it's all personal preference. After losing a few LO's thanks to misplaced PSD's, I'm going to start saving everything for web as well as flattening and saving the full size 12x12 and uploading right away for printing.