The basic principles still apply to inDesign, but ID may support more file formats than Freehand (which I have not used).
It is still a good idea to place images that are already sized properly for the use in the printed piece: a 5 x 5 inch image should be CMYK, 1500 x 1500 pixels in size, and cropped properly.
It is possible (and some say preferable) to place an RGB image. Indesign handles images that need to be resampled fine as well, and cropping is not a big deal, but for large image intense projects, it can still be a problem for your printer's equipment: a RGB 20,000 px square image that set in the document to print at .33 inches still must be processed (resampled, color interpolated) at full (data) size by the RIP.
If you are providing PDF files, then the export dialog boxes allow you to set (or disable) downsampling for images over a min dpi threshold. This handles your conversion for anything that doesn't conform to the rule of thumb above. Note that the PDF export embeds the image data which is different than "encapsulating a file" within the PDF. Because of this, the file storage format (TIFF, JFIF (jpeg), PSD) you use has no relevance to the recipient. PDF stores either raw pixel data or JPEG. Note that JPEG is always lossy to some degree and "jpegging a jpeg" is generally considered a bad idea, so it is again advisable to work with non-lossy compression formats when designing and avoiding the move to lossy formats until the very end of the process (the export) to prevent compounding of slight quality losses.
From an archive standpoint, TIFF is still fine and is well supported now and probably into the future. PSD files are supported but long-term version support is (in my mind) questionable. I have 15-20 year old catalog files here and only the TIFF (and SCT) files are openable on my work station.
Regarding "3mm borders for bookbinding", I presume you are talking about "creep" (accounting for paper thickness) and not merely the gutter margin. Usually you set your pages for the "trim size" and let the printer allow for creep when they convert it from "reader spreads" to "printer spreads." If you need to export a 100% "press ready" PDF then you should ask your printer directly.