I've accumulated a pretty sizable collection of tackle over the years. I do a lot of different types of fishing. At some point I decided that the best thing for me was to put everything in an Excel speadsheet. For each reel, I indicate what line is on it and for non fly reels, when I last changed the line. Also stuff like when I last did an overhaul (important for saltwater reels).

I mark the fly lines themselves by making rings with a Sharpie marker as mentioned by grumps. You can also arrange the rings in such a way as indicate WF or DT.