Best Graphic File Choice?

InDesign CS3 version 5.0.4 on a Mac.
I put together a multipage magazine and deal with various file types all the time, from advertisers, photographers, stock-photo sites, etc. I take what I can get and do the best I can with it, but if I have a choice when selecting the file type of a given graphic element, what is the best (cleanest, sharpest, truest color) for printing.
Examples:
Photo - Tiff, JPG, PSD?
Graphic - Tiff, JPG, EPS?
Prebuilt Ad - PDF, JPG, INDD?
I know this is a extremely big question, but would love to get a discussion going to help me make the best decisions down the production road.
Thanks
Greg

Native Illustrator files are superior to EPS files from Illustrator in every way, so long as you are using a program that supports them. InDesign does, QuarkXPress (at least up to version 7) does not.
I use only four formats for all my graphics:
Flattened TIF with no layers except the Background layer. I use this whenever I do not have layers in Photoshop so that I can tell at a glance how complex the image is likely to be.
Layered PSD for any image with layers in Photoshop. For the same reason as above, I can tell just from the filename how complex the image is likely to be. If I am supplied with a layered TIF I will either flatten and save as TIF (extremely unlikely) or save as layered PSD instead.
Adobe Illustrator AI files. Any vector file I am supplied with, except press-ready PDF, I will convert to native Illustrator files. See below for more information about this format.
PDF. Native AI files actually have a PDF file embedded, so saving as AI and placing that file in InDesign really means placing a PDF. I also use Photoshop PDF (with the PDP extension) for Photoshop files with vector layers, vector masks, and text. This allows me to keep more vecotr elements as vectors than if I use PSD.
All other formats I convert to one of the above, even if it is not strictly necessary. When I preflight a file I always flag JPG and EPS files, since I know just from the file type tht I have not looked at them and cleaned them up (if necessary).

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