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Another vote for Bookman here.
I used to use ComicZeal, but switched to Bookman for two reasons:
- Unlimited folder structure
- Transfer via builtin ftp server not just iTunes file transfers
It has been a while since I used ComicZeal, so it may now offer these.
If you are going to be reading at night, you also want a comic reader that offers its own brightness control, to go lower than the system one allows. Both ComicZeal and Bookman do this.
For handwritten notes, I've only played with these for a bit, but of Penultimate, Notability and Noteshelf I prefer the latter.
Penultimate does't offer a writeable zoom mode or palm protection, and of the other two I never quite got the hang of Notability's menus and options, Noteshelf behaved more in the way I expected it to.
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