I would like to be able to use a tool like WatiN to automate somethings that needs to interact with a Web App that is access by using an instance of IE running on Citrix. So far it seems impossible to interact with the window at even a rudimentary level using SendKeys as the internal UI components seemingly do not have a handle.
Has anyone been able to do this or anything similar?
Answer
You can try UiPath in order to handle Citrix automation (and also desktop or web).
Here's a full tutorial showing different Citrix automation techniques for data entry, data scraping or clicking and typing in virtual desktop environments.
You can use it from code (SDK) or create visual automation (workflow) directly from UiPath Studio.
Take into account that Citrix/virtual desktops are streamed to the client computer as an image so you can't have access to the UI tree elements.
Note: I work at UiPath so I know it can do the job. You should also try other visual automation tools like Automation Anywhere, WinAutomation, Jacada, use them side by side and choose the one that suits you the best.