First, by default, ID uses a low-resolution preview on screen. You can change that with View > Display Performance > High Quality Display (and you can make this the Default in your preferences).
Second, 144 ppi is barely adequate for low-resolution printing on a desktop device at 100% scale, and your text will be impossibly pixelated. 72 ppi will be horrid, and if you scale these images larger they will only get worse. For press output the rule of thumb is an EFFECTIVE resolution of 300 ppi at print size, and you can read the effective ppi in the info panel with an image selected. Text at 300 ppi, however is still going to look pretty bad, and you may need to go to 600, 800, or even more. Note that the image needs to be captured at high resolution. Upsampling in Photoshop will not work.
I would try to save the images as PDF in Photoshop and place the PDF in Indesign. Or better, if you can save the original images as PDF and place those in Indesign.
This info was quite helpful--thanks everyone!
First of all, I'm not entirely sure I chose the right tool for this job, and advice on this would be welcome. I wanted a document of portfolio pages formatted sort of like a book, so I thought it would be better to use InDesign rather than something like Photoshop or Illustrator (I've learned these tools in the last year but haven't really used them to create documents). My primary goal, however, was to present this information both from my computer and on my website, and a secondary goal was for it to be able to print nicely. So I thought InDesign was the right choice. (I read this article from 2010: Adobe Photoshop vs. Illustrator vs. Indesign | Dream Infinity Studios / Chris Takakura | Art Direction + Design to get some guidance...hopefully most of it is still relevant.) Because of that I wasn't sure whether to use "Intent" -> "Print" or "Intent" -> "Web", so I went with web with a 1024 x 768 page size, hoping that will look OK for desktop (not professional) printing. What do people do when they want something to function in both domains? Not sure if that could have affected anything about the way these images were placed...
In terms of finding a solution:
1. I was using High Quality Display--it was more an issue with my output document. (Though strangely sometimes when I toggle between high-quality & typical displays, sometimes things that looked good when I was working on them in high quality, after toggling to typical and back, look horrid.)
2. It seemed at first that it might be an issue of the way I placed the files, e.g. I was positioning my cursor OUTSIDE any sort of field and dragging a square to the size I wanted my image to be. I'm wondering if it somehow reduced the image size because if I create the square using the "Rectangle Frame Tool" it seemed to work much better. I've also tried just dropping the file without the frame tool and resizing it that way, but my images are actually VERY long & wide, so that's difficult. I was also wondering the "fitting" option I chose may have been affecting the display...I've been trying "Fitting" -> "Fit Content Proportionally" lately.
3. I created some .pdfs of some of the pings from Omnigraffle, and that seemed to help, but that actually makes them look worse because there are screenshots within the OmniGraffle mock-up files which are washed out and pixelated and the text that was added on top stands out too much (see attached screenshot...the one on top is a PDF and the header and footer looks funny and the bottom is a PNG where at least everything looks consistent).
So though some files look better now (especially, ironically enough, the 72 DPI screenshot of Use Cases!), I can't figure out what process I should follow to get consistently good results. Because a) the mockup files look good when I first paste them, and b) they are longer and wider than the content area I'm using and I'm shrinking them significantly, I cannot figure out why I can't keep that level of detail after they've been shrunk to fit. I keep wondering if I'm placing image properly, shrinking them properly, or those Fitting settings properly...
Basically, screen shots will always look exactly like what they are, low-res images of the screen. You will never get smooth type in a screen capture unless the area is zoomed in very tight to give you lots of pixels for each glyph, and that's not helpful to see the whole window.
I'm not the person to give advice about designing for screen as I work strictly in the print world, but in general you probably want to start with a file that is adequate for print (set the intent to print and use images with appropriate resolution if you can, screen caps being the exception). You can reduce the resolution in a PDF for screen. Screen caps are best used at 100% scale. If they need to be scaled, do it in ID, not Photoshop, is the advice I see here most often from folks I respect. You do tend to lose details on screen when you scale smaller. Remember that your screen uses pixels, and you can only use a whole pixel for a particular color, so if a detail becomes smaller than a single pixel on screen it will either disappear or be magnified to fill the pixel.
I noticed that Acrobat uses 96 PPI for it's resolution when viewing images.
Therefore, for any PDF for the web I always have the images at 96 ppi or higher.
72 PPI images always look terrible - I place screen shots at 71% original size to accomplish a better look for viewing on screen.
And for printing Screen Shots, I've often retyped the text and rebuilt the design to get a better reproduction.
So, is the first image in your original post the actual screenshot at full size, the last one a screenshot of what you see in the PDF from InDesign?
The original screenshot looks fine for what it is, a screenshot (I think that screenshots should usually represent what you'd see on screen).
I think the problems you're seeing are down to your Display Performance settings (switching to High Quality should improve that), and more importantly, your PDF Export Settings are downsampling your screenshots. In the Export Adobe PDF dialog box, navigate to Compression, and try setting everything to 'Do Not Downsample'. This is presuming your images are all screenshots, and there's no large photographic images or anything that might bloat your PDF. You might want to play with the compression settings to see what yields your preferred balance of quality and file size.