I think we can all agree that whoever finds this message in 50,000 years isn't going to speak English. Or Mandarin. Or Hindi, French, Spanish, Swahili, or, in fact, any language spoken today. So we'll have to figure out a way to communicate with them in a language that we'll both understand.
I'd look to communication with aliens for inspiration. There have been various proposals involving math. For example, we could perhaps use prime numbers in an attempt to show patterns. Any sufficiently advanced civilization could understand that. Or perhaps we would use a modified version of binary code. Maybe we could just decide to create a new language, that would be easy to decode.
To preserve this message, we need to put it somewhere that will protect it for a long time, but will still be open-able in 50,000 years. Paper is, of course, a good choice, but it can degrade in certain environments. Etching the message in metal is another option. Sure, you could store it digitally, but all digital devices have a limited lifetime - certainly less than 50,000 years.
We could encase it in some hard material, such as metal or stone. I know that some smart-alec is going to say amber, so I'll add that here. Essentially, you need something that will survive 50,000 years untouched by the things around it - i.e. a material that's tougher than its environment. Perhaps you could put the message on a sheet of metal and encase it in pure diamond. That way, whoever discovers it could maybe read it through the diamond. Alternatively, put it in a solid glass box and encase the box in some tough, transparent material.
All the ideas above can be summarized like this: Write the message in an easily-decipherable code on a stable medium, stick it in something that will last a long time, find a safe place to put it, and wait 50,000 years. There is another option, though: send the thing to space.
The KEO satellite will (if the project ever gets anywhere) stay in Earth orbit for 52,000 years. It will then re-enter the Earth's atmosphere and, hopefully, carry a message to whoever is still on Earth at that time. (The LAGEOS satellites will also enter the atmosphere - albeit it 8.4 million years from now; their primary function is also not that of a time capsule) You could do something a la KEO and put a message in orbit, where it won't be impacted by severe weather, continental drift, or those pesky humans.
