Thank you David!
I already have an app from Omni Group on my Mac, it's called Omni Outliner and I have been using it for years to make to-do lists. I'm not sure how much more Omni Focus offers though, and it's rather too expensive for the use I would put it to I think. I thought about buying Omni Outliner for the iPad but well, I'm not sure how well syncing between the iPad and Mac version would work. Plus I'm not sure I could attach external files to a list in the iPad version.
Good suggestion about trying the Mac version of Bento, I may do that.
In the meantime I bought a cheap app called Next! I paid 0.79 € for it, I don't know if it's the regular price or a special Thanksgiving offer. At first sight I hated it, but I tried some more, finally figured out how to edit an action (the interface is extremely confusing at first) and type a note, and I think I'll keep using it for a while. At least it seems to cover my basic requirements: notes, to-do, file attachments. The interface is obviously optimized for a small screen and on the iPad, at least half of the screen surface is simply not used, which is rather frustrating. If they ever make an interface optimized for the iPad, this could become a good app, depending on how much they sell it for.
I was even able to find a convoluted way to read an attachment I received in .docx format, which I can't read on my Mac or in the iPad's mail app. I opened the attachment in Goodreader (this app is really useful for so many things) and sent it to Next, and now it's attached to my project. And readable