For sure doing it all in a layout program is best. Lets you set up the pages so that photos are sized, rotated and edited.
But another option for Windows, you can get Cute PDF and print files straight to PDF. There is a free version but I don't know the limitations, we ended up buying it because it's used for a business. None-the-less, it allows printing of several pages to a single PDF and this might work if you're scanning pages since you would not have to change the dimensions. IOW, taking a magazine page to a PDF page of the same size would require just scanning, cropping and printing all to the same size.
Mac OS X has this print to PDF feature built-in if you happen to be using it.
The quality is acceptable, you do all your editing on the photo side and don't have much control over the PDF quality. We have an aging version of Adobe CS that includes Acrobat Pro 9, so if you need PDFs edited and joined let me know.
BTW, you can use GIMP, which is free, if you don't have Photoshop and want something fairly close in function. IIRC it has a plug-in for removing the halftone and de-aliasing printed material.