This is the Elitist Jerk in me coming out for a minute:
"The best 60 minute workout builder is your brain."
Admittedly, this is only useful advice for folks who have already gotten a fair bit of familiarity with the various exercise options available. Call it "intermediate to advanced advice."
Nobody knows your goals better than you do. Nobody knows your body better than you do. Nobody knows how you feel on a particular day better than you do — if you're ready to kick butt, why limit yourself to the workout that some app or piece of paper says you "should" do if it's an easy day on the program's schedule? If you're having one of those days where just showing up is an accomplishment because you slept like crap, or lunch is sitting funny, or whatever, there's no sense in killing yourself excessively.
What it sounds like you're looking for is a programming app. I don't know if there are any with any sort of learning curve (the way Yourself Fitness or Wii Fit or other PC/console applications have) for mobile devices.
Basically, you've got a hierarchy of priorities that will shape your thinking.
Overall Goal: This is the broad, all-encompassing bracket; think of it as the game system (d20, etc). Stuff like "losing weight," "getting stronger," "running faster," whatever.
Current Phase: This is the module (program) you're involved in. If you're doing a particular workout plan that says "Wednesday is leg day" or "Add some intervals to your run," or something like that.
The Daily Self: How you doin'? If you're feeling like gangbusters, go strong. If you're feeling off, do what you can.
Regardless of what you end up with, it should fit into your overall goal, and the current phase of what you're doing to achieve it.
I may wake up with a particular workout pencilled in my log book; when I walk into the gym and put my hands on the weights, however, that may or may not dictate what ends up getting done, to varying degrees of adherence.
This approach tends to work just as well for strength training as it does weight loss, in my personal experience (this will change when my focus shifts to more running and less lifting).
If you TL:DR this, so help me…. 