I'm sure there may be better options than what I've got here but two that immediately come to mind are:
1. Kinetic - this is the app that works with my trainer. It's free and worth every penny (i.e. it's pretty mediocre).
2. Zwift - only beta version on android, but it seems to work fine based on youtubers showing demos. Of course, this costs a fair amount, so I'd say look elsewhere unless you want to have the full zwift experience. You can probably find a cheaper way to just do structured workouts.

I'm pretty sure you can program structured workouts in apps like Cyclemeter and IPbike. I just haven't done it.