What do people use today?
Play Books automatically syncs your reading progress, notes, bookmarks etc and there's no additional overhead on your part.
I wish Amazon allowed syncing of highlights / bookmarks for uploaded books.
We will later also allow you to import your Kindle highlights and notes.
We're working on EPUB. We want to do it right so it's taking a bit longer. A lot of our users are using Calibre to convert from EPUB to PDF.
We've seen a LOT of uptake among students/academics so PDF has been the main focus so far.
We also have HTML capture and are working to unify the EPUB and HTML capture functionality.
We're trying to be far far more than a reader and view polar as more of a spaced repetition platform with integrated reading so that it's insanely easy to read while learning using spaced repetition.
Anyway... if you have any questions AMA.
Since we (Polar) got our start here on HN (https://news.ycombinator.com/item?id=18219960), Kevin and I decided to give anybody who signs up 2 months free premium (valid until Jan 31, 2020). Just respond to my welcome email when you sign up :)
IIRC, recent development to polar was to make it much more friendly for viewing on mobile.
We're working on finishing reading up on mobile too.
then we're going to package it as a native mobile app.
And you get a free year of cloud storage if you make a non-trivial contribution.
I use this AppleScript trick + rmapi  so I can use the native Mac print dialog to print to remarkable. Basically, anywhere I can print a PDF, I can print to remarkable the same way.
I installed Printopia  on my mac to host an AirPrint server on my local network, which can share the print extension I created to print to remarkable. So when I'm on my wifi, on my phone, I can use the native "Print" functionality to "print to remarkable" via AirPrint on my laptop.
The only thing missing is the ability to get this setup working when my phone is not on WiFi. I've installed ZeroTier on phone/mac, and connected them to the network so they can ping each other, but I'm having trouble getting mDNS to work properly. The laptop is sending the packets to the ZeroTier interface, but the phone is not receiving them for some reason. Not sure if it's expected, since iPhone Network Extension can only setup the equivalent of TUN interfaces, not TAP (which is needed for L2 AFAIU).
 https://www.decisivetactics.com/products/printopia/ -- It's $20 but it works really well. I played around with setting up my own CUPS + Avahi server, but getting it to work in docker was a pain, given the native OSX CUPS server was interfering and some other issues... Printopia just works.
One question, if I may: is there any way to import screenshots (ideally .png files) into otherwise handwritten remarkable notes? I use this functionality fairly often on my Chromebook (doing screengrabs with the stylus, then embedding them into otherwise handwritten Squid  notes, sometimes annotating them, then exporting the entire note as a PDF).
Workflow- for kicks I wrote a little utility using the unofficial API so I can send PDFs to their cloud service from my laptop, and plan to deploy it with an AWS SES inbound thing so I can email PDFs and have them show up on the device, like the kindle service. I expect also to PDFify my kindle books so I can move them over as well.
This isn't a cross-device solution as the OP requested but I find using a single dedicated reading device works better for me. Very happy with the remarkable.
$500 is just a bit steep...
I don't have a solution for synchronization at this point. My current workflow is quite involved: import a document into Calibre, upload it to Kindle via Calibre wireless connection (KOReader supports it), read and highlight, get the modified doc back to Calibre, extract highlights with https://github.com/0xabu/pdfannots. It'd be more convenient to send new highlights from Kindle somewhere immediately without transferring the document itself. I haven't looked into it, but I believe it should be possible with a KOReader plugin.
You might be interested in replacing your paperwhite with a "boox" or "likebook" ereader device. Both of these run Android, so in addition to koreader you can install e.g. syncthing and have a shared directory copied between all of your devices and your own PC.
Also bonus - support latex and bibtex. You can highlight in the pdf, and zotero will extract those highlights and add them to the entry as notes. Very handy.
And for mobile, i use this seemingly now-abandoned app called papership [ios]. It lets you signin to zotero and your webdav provider, so you have a sync of books/papers, along with your highlights, notes and whatnot. Thankfully, it seems like zotero are hiring ios devs, so a first party app might be on the horizon.
edit: seems like papership recently started getting updates again, so its not abandoned anymore.
I basically use Dropbox as a back-end, using Autosync for Dropbox (fka Dropsync)  on Android and ChromeOS (and the vanilla Dropbox Linux desktop client on Kubuntu) to keep the files synchronized (storing them on SD cards on my phone and Chromebook). I have it automatically sync frequently, and the app automatically uploads local changes to the cloud.
For PDFs, syncing the highlights is of course trivial; as a reader, I use Okular on Linux and Xodo  on Android/ChromeOS. Xodo has more features -- I like using my Chromebook's stylus to scribble notes in the margins -- and everything ports well to Okular, and vice versa.
For EPUBs, I use Calibre on Linux and Moon+ Reader Pro  on Android / ChromeOS. In practice, though, I use the latter almost exclusively; it has a built-in Dropbox sync functionality , though I'm not sure the highlights etc. are accessible by other apps.
BookFusion currently allows you to easily upload,organize and sync your eBooks across Android, iOS and Desktop(via Web). All your highlights, bookmarks, notes and reading progress will always be synced.
More at: https://www.bookfusion.com/reading
Calibre plugin: https://www.bookfusion.com/reading/calibre
There are some gaps and features that are missing but they all will be filled with our new release in Q3 2020.
After that it's available everywhere including my mobile phone and kindle reader which makes it quite easy to remain in sync (bookmarks, highlights, last page, etc)
We also have a Calibre plugin https://www.bookfusion.com/reading/calibre
I have settled with Notability due to its nice iPad app where I use my Apple Pencil to annotate - the annotated PDF syncs to iCloud so it's available on Apple products (don't think it supports Android/Linux so maybe not cross-platform but something I'd recommend checking out if you can live with that limitation). If it's a book I'm using to learn something (usually tech), I then transfer notes to Bear in outline format (using the Notability mac app to read notes) and sometimes Anki for flashcards. One downside is that Notability doesn't support ePub so I either convert those or read on Kindle.
I tried OneNote recently but the iPad app seems unable to handle larger PDFs like textbooks which is a major bummer and surprising to me.
For everything else, I use Calibre and the standard PDF reader that comes out of the box with Ubuntu. I keep notes, highlights and bookmark indications in separate Google Keep notes, one note per title or, sometimes, one note per "subject", which would include various books and articles I'm reading. The method sounds like extra work, and it is, but it's rewarding because Keep is very flexible and easy, its tagging feature and "searchability" work fine.
I use Kybook 2 on my iPad. I think Calibre supports syncing with Kybook 3, so you could try that.
If you really want highlight syncing etc, it might be worth migrating to a Kindle-first workflow? But PDFs aren't there.
Why is this so hard :( Why can't everything use a standard progress sync protocol? (KOReader's is at https://github.com/koreader/koreader-sync-server)
BookFusion allows you to upload and manage your eBook collection across Android, iOS and Desktops. All your eBooks, bookmarks, highlights, notes and reading progress are always synced across all devices.
More at https://www.bookfusion.com/reading
Calibre Plugin - https://www.bookfusion.com/reading/calibre
Send to Kindle - https://blog.bookfusion.com/how-to-quickly-easily-transfer-e...
There are a few gaps but a brand new and refreshed platform is being launched in Q3 2020
Right now, I support sharing via my own Ubooquity/elibsrv servers which run OPDS as well. OPDS works well with Kybook, which is what I run currently on iOS.
Unless this supports an OPDS server, I don't see myself using this long term, though. OPDS on Kindle (with KOReader) makes my life so much simpler (I can browse my entire collection on the Kindle).
Kindle syncs PDFs. You have to email them to your kindle email address, but they work out of the "Documents" section. And they sync as well. As far as I can tell, anyway. I don't really do any highlighting, but the docs are available.
KOreader fixes some of it, but you lose the highlight sync.
Single columns have worked great, though—if you don't rely on colour, of course.
Also, you could upload your PDFs and you would have a simple online library.
I just discovered Foliate[0,1], which is a very small reader (252kb, deb) for .epub, .mobi, .azw, and .azw3 files. It's based Epub.js. I was looking for a standalone epub reader (wanted to avoid the document management stuff) and stumbled across this gem.
It's performed very well on the epubs I've tossed at it.
BookFusion is exactly what you are looking for. BookFusion allows you to upload, organize, manage and sync your eBooks(PDF,EPUB, MOBI and several other formats) across iOS, Android and Desktop(via Web). All your bookmarks, reading progress, highlights and notes are always synced across all devices.
More details at https://www.bookfusion.com/reading
Native iOS and Android apps. We will be releasing our native cross platform app in 2020.
PS: Founder at BookFusion. Will be happy to hook the HN crew up. Let me know if you have any feedback. Tons of improvements and new features coming in 2020.
There are a lot of publications like Manning also have Dropbox integration, and automatically deliver new copy every time when new versions are available.
This set up is far from perfect, but I have liked it more than trying to use Devon think or other tools, because I can still easily access all of the PDFs in the file system. I am really curious to learn about other workflows.
Then, since it's org mode I can organize and edit the notes.
At one point I think i will give up on Kindle as a book reading and go all in for the iPad and I will switch to Apple Books but I think i will still export the highlights to somewhere.
If I really need sync of progress, I either rely on something called memory, or work from Calibre's built-in webserver.
For pdf's I usually just use SyncThing (but I don't have bookmarks there), for the rest I use the various apps. I am considering trying out Mendeley again, that is geared more towards researchers, but works cross-platform :-)
Works great. Has all the research papers I read. Dunno about synchronizing highlights, but airdrop makes it simple to get PDFs on and off my phone.
1. Creating a Custom Series and then adding each book. Example Scotts List
2. Create a virtual shelf and then add the books there - https://bookfusion.zendesk.com/hc/en-us/articles/36003058387...
More about BookFusion at https://www.bookfusion.com/reading
Works pretty great
Wish some form of ePubs would replace pdf’s.
I want books published in a better format. Too many books are pdf only:
ePub is an HTML format. It’s just not sufficient
But yeah AFAIK it's apple only.