Back at the dawn of time, when PowerPoint was first being programmed, a fateful and incorrect decision was made. Placeholder content would always appear in front of static content, regardless of how placeholders and other content were stacked on the layout. This has led to countless bald designers, from them tearing out their hair because there's no way to place logos over photos.
The Locked Graphics Workaround
One way to circumvent this design flaw is to place a picture placeholder on the layout as usual. Then create a sample slide from it. Place the logo over the photo and lock its position in the XML. Here's my article on how to do that: OOXML Hacking: Locking Graphics. This allows the user to replace the photo while keeping the logo in front.
The disadvantage is that you can't create a new slide from the layout. Instead, the user must copy and paste the sample slide to create another one.
The Background Picture Fill Workaround
If the photo is a full-screen photo, there's another method. This time, don't place a picture placeholder on the layout. Instead, just place the logo there. In use, the user right-clicks on the background and chooses Format Background. On the Format Background task pane, choose Picture or texture fill, then click on the File button and choose the background photo. The logo will stay on top.
The disadvantage to this technique is you have to include instructions to the end user, who may never have used a picture fill previously. My thanks to Jaakko Tuomivaara of Supergroup Studios in the UK for this tip.
Logos Over Photos: The Placeholder Picture Fill Workaround
This works with any size photo, it doesn't have to be full-frame like the previous hack. No copy and paste, no instructions required. I heard about this one from Joshua Finto (Make It So Studio in Austin, TX).
On the layout, insert a picture placeholder to hold the photo. Then add another placeholder on top, sized to exactly the same size as the logo. I use Online Image placeholders because they are rarely used, using a common placeholder type risks content being placed in it if you change layout types. Remove bullets, if there are any, and type a space character so no placeholder text appears.
In the Format Picture task pane, click on Picture or texture fill, then on the File button and fill the placeholder with the logo. Create a slide, place a photo and voila! The logo appears over top of the photo! After creating this, it's wise to lock the placeholder in XML on that layout, to prevent distortion by the user playing with it. OOXML Hacking: Locking Graphics. EMF, SVG and transparent PNGs are all good logo formats for this application.
Microsoft maintains User Voice forums to collect feedback from users. I've created a suggestion there that the placeholder/shape stacking order on the layout should be respected on slides. Please add your vote here: Layout shapes and placeholders should keep their stacking order on the slide. Perhaps we can persuade Microsoft to fix the mistake so we don't need these time-wasting workarounds.