The answer is indeed “whatever works for you”.
I don’t use Lightroom. I downloaded the 30 day trial and loaded in a couple of day’s worth of photos to experiment with. Performance seemed pretty good but I couldn’t print the way I wanted to. Then I used Windows Explorer to move the photo files onto one of my storage drives. The next time I started Lightroom, it said it could not find my files and was deleting the information from its database! The result was all my edits in Lightroom were gone. Those two strikes against Lightroom were enough and I uninstalled it. I have never been a fan of proprietary databases because they usually end up costing me a lot of time when the developer issues an upgrade that uses a different arrangement.
Lightroom is a browser that has ACR and some additional editing and printing features added on. Photo Mechanic is not an Adobe product. Photo Mechanic is pure browser.
Photo Mechanic is a lot like ZoomBrowser EX, but it is faster when dealing with large numbers of large raw files. Photo Mechanic has sorting and filtering functions. If you choose a file to edit, it passes the file to the program you have assigned as your editor.
I have used Photo Mechanic a couple of times when I had thousands of files to sort through and because they were all from a single shoot, they were all in the same folder. I have a folder per card when my program reads cards. These are aggregated into either a project folder, daily folder or monthly folder depending on quantity. Trips usually get a folder for each day, as do events and projects. Everything else usually fits in a monthly folder. ZoomBrowser EX came with Canon cameras prior to the 1Dx/5D Mk III, which shipped with a new browser, ImageBrowser EX. I like ZoomBrowser EX better, so I still use it most of the time.
I attended a bridal show in January, and took 1001 frames plus half a dozen movies. If I open that folder in ZoomBrowser EX and scroll to the bottom, I have to wait almost a minute for the thumbnails to be created. If I had 5000 photos in the folder, I might as well go for coffee. As you scroll down, in a big folder like that, Photo Mechanic can still keep up. I have over 200K of digital files, but I try to keep less than 500 in a single folder. I have folders arranged by year, then month, then day/project/event. That works well most of the time. Weddings and trips sometimes result in 1K or 2K being in a folder. Weddings can be broken into pre-wedding, wedding, post-wedding, and reception, if I need to improve browser performance.
Since I use Photoshop CS5 as my editor, raw files are handled by ACR and I get the XMP side-car files that hold the editing information. When selecting files to be edited, I use Bridge which comes with CS5. As long as I move both raw file and side-car file, together, I can use any tool I want, to move the files without offending some proprietary database. Over the years I have probably had a hundred photos where I wanted to save the editing information. Sometimes that has been done by saving intermediate JPEG files while using Elements, sometimes by saving a PSD file from CS5. Digital Photo Professional asks if you want to save your edits, sometimes I say yes, sometimes no. It writes the changes into the file, but you still have the original raw data so you can always go back and start over. If it only took a minute or two to decide on white balance, exposure, fill light, recovery, perhaps noise reduction and lens correction, then is there a huge need to save your edits? On the other hand, if you are doing editing in Photoshop and you have a composite with 10, 20 or a hundred layers, perhaps there is a point to saving your edit. Usually the PSD file is huge, but it saves your layer information so you can go back and continue editing where you left off. Most of the time, I finish a photo in a single session, produce a JPEG the size I need, print or post it and perhaps add it to the slide show my screensaver uses. Once done, I seldom go back and edit that photo again, so keeping editing information has never been a selling point I paid attention to.
Over the years I have used various programs and had several different work flows. Even in a single editing session I may use different work flows. This is very evident at the moment because I don’t have CS5 configured to convert my wife’s G16’s raw files, so from last week’s photo session, my files are converted in ACR, and hers are converted by Digital Photo Professional, before being passed to CS5 for cropping and printing.