Updated 4/5/2019
I spend a lot of time reading articles for research–these articles are generally pdf files. I’ve tried several different annotation packages for the iPad.
Note: I have no interest in reviewing apps–lots of other people do that already. However several people have asked what apps I use. Your preferences will vary.
iAnnotate PDF
Update: I purchased the new version, which does include an iPhone version. The most recent update even includes a scanner app. This is still be best PDF annotation package I have tried (but do note that the iPad can now do some of this without extra software).
Original Review: This is the first app I bought for an ipad. The interface had changed quite a bit since then. There are plenty of tools–almost too many –but the interface makes this work. You can search WITHIN the text of all pdf files downloaded to the app. I appreciate how easily this syncs with various cloud storage providers. For example, you can just press the sync button and all annotated files will be synched to the provider of choice. If you delete a file from the device that file will still be on the cloud server. There is no iPhone version.This is my first choice.
PDF Expert
I acquired this app in a bundle with several other packages. It’s a universal app and works well with other apps from the same company. This provides good basic annotation abilities but the search and sync functions are lacking. I do like the signature function.
GoodReader
Lots of people love this app…I decided to try it when it went on sale for $0.99. The basic tools are there but I don’t like the interface. Sync is just not good. If you sync a file to a cloud storage provider, deleting the file on the device will delete the file on the server (glad the app warned me). To delete the file only from the device, you must first unsync the files.
PDF Forms
This was a free download of the day. It’s pretty comparable to PDF Expert.
Other options
Many note taking apps can import and annotate pdf files as well.
Update: if you want a combined app, consider GoodNotes.