Which coin to mine with CPU long-term I have a machine with 48 CPU cores, running Linux. I would like to mine for a coin, not to sell immediately, but in several months when the value has increased (hopefully).

I don't want to keep changing every day, so what coin would be best, and why? I realise this involves predicting the future, but would like to hear various views.
Generally, CPU mining isn't worth the electricity consumes.  However, we will assume that you've got some adequately efficient cores.
If you are going to do CPU mining, you might have more luck using a scrypt based fork of bitcoin, such as tenebrix, litecoin, or fairbrix.
Because the effectiveness of a setup can vary, as well as the price of various cryptocurrencies, your best bet is to do your own experimentation:
 
For each coin:


Mine for an hour or so, and determine your average mining rate
Look up the current difficulty of that coin
Use something like the Bitcoin Mining Calculator to determine how much you stand to make 
Convert it into $ per day or something similar


You would then compare the profitability of the various coins and choose which is best.

Alternatively, if you wish to assume that scrypt is best for your setup, and that your hashrate will be identical across different scrypt-based coins, you can use CoinWarz to determine the best coin to mine (currently Fastcoin, although they rate fastcoin as having bad stability, so you may wish to drop down to digitalcoin or novacoin if you feel like you need something a little more stable.)