Can't help you about comic books since I use one with a DRMed proprietary format (I think) by Comixology.
For notes, I tried a lot of apps, and I ended up using Notebooks for typed notes, and Noteshelf for handwritten ones.
I gave a review of Noteshelf in
this post.
Regarding Notebooks, I don't know if it would answer your requirements. I use it to write notes and manage small projects with to-do items and checklists. It's simple but, in my opinion, rather powerful in its simplicity. The idea is you create books, and notes inside of books (you can nest books inside books). A note is either a simple .txt file or an attachment that you can import from other apps: images, pdf files, MS Office files... If your book is defined as a check-list, each note also has a status (not started, in progress, done, cancelled) and an optional due date. You can save your books and notes in Dropbox as folders and .txt documents, which means they are readable without using the app, I like that, it means if for some reason I can't use the app I will still have access to my notes. Anyway, I like this app and use it every day.