Evernote? Good to go just about everywhere on just about any device or computer.
If you intend to use it offline much, you'll probably want to spring for the premium account; less than $5 a month.
If that does not appeal, there are lots of PDF reader and annotation apps. iBooks will let you keep PDF files, if all you intend to do is read them. I use GoodReader and PDF Expert for PDF files that I might want to do something more than read.
Pretty much any notes app can be used to keep a list of links. I'm not inclined to trust the native Notes app with this, as it's been known to lose notes (not me, but other's have).
Another possibility, since you most likely already have a Google account, is the Google Drive app. You can store and view PDF files, and keep a list of links in either a word or spreadsheet document. Individual files can be marked so that they are available off line. You could start with this and then take your time looking around for apps that meet your needs more completely and conveniently.