The free transcription tool at
http://www.jacobboerema.nl/en/Screenshots.htm looks interesting and I suggest trying it.
An alternative (page by page) solution might be to use a photo editing tool and type in a 'text layer' over the original document image (PDF, .jpeg, etc.). This is not something I'd recommend (it's an overkill) but depending on the types of documents you work with and what you want to do, it might be an approach to consider.
I attach a screenshot illustrating this approach with Photoshop but there are other (free/cheaper) tools that do the same thing . GIMP (which I use from time to time) is free and for typing in a text layer works the same as in Photoshop.
The steps are:
1. open or more separate document pages (PDF, .jpeg, etc.)
2. on each page (by page), click on the 'text' button. This opens a new ' text layer' above and separate from the original document.
3. draw a text 'window' on the text layer over the original document (or the parts you want to transcribe)
4. Type your transcribed text in the text layer 'over' the original document.
6. Save your 'work in progress' and final versions with the document and/or copy and paste your transcribed text to a different format (Word, website, etc.)
You can of course create multiple text layers (one for each section, or annotations) for a document page. By copying and pasting transcriptions from multiple pages into something like Word, you'll get a multi-page transcription in one document.
I don't do much transcription so I'm not sure how efficient this is. In the attachment, the original text is old Flemish. Again, this is not something I'm recommending, just pointing out that this kind of 'solution' is available too.
Mike