Creating a preflight profile is a good way to manage your files for print. You can tag resolution, color space, fonts, links, trim and bleed, etc... The following is a discussion on some of the settings you may want to consider when creating a preflight profile in Adobe InDesign. Of course you will want to check with your printer to make sure these values are appropriate or they may even have a profile they can send you.

One of the first sections you can check off is the links section. In addition to issuing a warning about missing links you can also flag the transparency blending space. The Transparency Blending Space is the color space (RGB or CMYK) that all colors in the document must be in order to insure consistency. If you are going to use blending modes, drop shadows, Bevels, Gradient Feathers, etc... you need to understand how that object will interact with the other elements on the page. Type can be unintentionally rasterized if it is too close to an object with transparency (for this reason it is a good idea to have ALL type on a separate layer and have the type layer on the
top of the stacking order, in the layers palette).

Color is always an issue and many printers no longer want "native" file formats and will only accept PDF files for print. That being said, I cannot tell you how many discussions I have had with students about color and how many complaints I have fielded about the printer ruining a project... Designers just remember that as much as you complain about how printers are destroying your projects; Printers are laughing about your lack of print savvy!
When I teach Photoshop I tell my students to always work in RGB, even if the final destination is print! Why, because CMYK and Photoshop layers are not always on good terms, because you won't be able to use your plastic wrap filter, because not all of your adjustment layers are available, because none of your digital photography profiles will match your color space... The list goes on and on. I teach my students to work in RGB and when they are done save their RGB file and maintain their layers. THEN flatten a version of that file and convert to CMYK. So the result is a file in RGB space with layers intact that can be edited if need be
and a flattened version in CMYK that can be placed in InDesign. Why go to all this trouble? If you convert to CMYK in Photoshop you have a better color engine and you won't be surprised. Also if you convert the flattened file you will marry all of your composites AND blending modes change from RGB to CMYK so it's best to "bake" the look into a flattened file. Finally, if you start with RGB, with it's larger color gamut, you will have a more vibrant image for your website (because of course you are going to use this piece for print and web...).
Spot colors are a different story. You will notice that my profile only allows for one spot color. Your project may have more but I have seen files with 25 spot colors (not intentionally). Be aware that when you specify a Pantone color for a swatch that you can choose spot or process and process, for the most part, is the way to go.
I also have warnings for overprinting and registration. You NEVER use registration in a project. It is there to be used by the software to print the Printer's Marks and is mixed from 100% of CMYK. No paper can hold 400% ink but on a tiny registration mark it does the trick. If you need a "rich" black ask your printer. An example would be C 70% M 40% Y 30% K 100% and this would only be used on large background areas and never for type (unless it's huge).
Overprinting is tricky. By default when you place one color on top of another the top color "knocks out" the bottom color, where they overlap. If you apply a blending mode like multiply of you set the Attributes of an object to overprint you and telling InDesign to let these objects blend. All ink is somewhat translucent so blue over yellow will produce green. If you do this it is importing to turn on Overprint Preview from the view menu. Lastly, white or paper is not a color in off set printing so be careful on how you use it. In general it is the color of the paper so if you paper is not white neither will the swatches assigned to paper be white.