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DesignJot App for iPad.
It's possible that DesignJot fits into this category.

This is a paid app ($5 aprox) focusing on analysis and set-up. Though aimed at corporate training design, I think it will be very useful for
working out your own instructional design product from scratch.
There are templates with typical questions already entered for you which I would find helpful (but check out the review below which criticises the app for being inflexible).
You can elaborate on these or create more of your own.
Even if the app doesn't work on your iPad (note it can only be used on the iPad) the information from the company site is interesting and useful.
Try Allen Communication Learning Services
Here's a recent quote from their blog How Social Media Should Drive More Authentic Training and eLearning. "We could be more transparent in how we present the need for performance improvements. We could involve the group in developing our performance goals and learning objectives. Let the motivation evolve organically from honest employee reflection."

If you download the app, you can navigate to the website from the home page by clicking the rather obscure icon set down low - or from other pages, the same icon is high up in the far left hand corner of screen. This is where you can get an idea of the principles behind the app. Worth reading in its own right, even if you don't have an iPad.

On the app itself, the tabs are categorised into Audience, Needs, Strengths, Weaknesses, Expertise and Results (ANSWER!). Each category comes with a Tips section plus a very quick (blink and it's over) video by instructional designers - I really wish they had spoken more slowly :-(

Typcially, a category (let's take Audience) asks, who they are, what they do, how they feel (tabs running horizontally) and within these sections there are drop-down menus with more questions for you: create, edit, delete or star. Along the bottom of the screen you have more sections - Analyse, Design, Notes, Sketch.
There's some useful guidance. For example I was impressed by the Design tab which opens to a flow chart (to make sure your course stays focused and relevant).
There are many areas to this app I've yet to explore. The test will be when I have a real project to use it with.
It takes getting used to as there doesn't seem to be a clear path through so I'm still playing with it and working out where things reside in relationship to each other....
One plus - at least there's a broad colour spectrum to choose from so your projects can be differentiated from each other.

The last word from eLearning Uncovered.

"My feeling is that this app would be more helpful to beginners than experts. But even for us experts, anything that helps us do more analysis is a good thing. And if this app has anything whatsoever that will help you with your job, it’s a bargain at $4.99.

As beginning designers need less scaffolding, though, my sense is that their own templates, created or customized using regular word processing, spreadsheet, presentation, and mindmapping tools, will serve them better. Those instruments won’t have the app-like experience, but with the ability to customize them, designers can make sure they meet the needs of their organizations and reflect their continued learning about instructional design."

eLearning Uncovered Book.
eLearning Uncovered
Check out this site for more ideas on a web-based instructional design tool.
"E-Learning Uncovered: From Concept to Execution covers the basic concepts you’ll need to know to take a self-paced e-learning course from concept to execution, from up-front decision-making to heads-down writing to review cycles to implementation."

Read the article 15 resources for free online education videos