What should I do with pokemon or candies that I cannot use

The only use for candies right now is to evolve pokemon and to power them up. Future generations will have more evolutions (for example Golbat, Zubat's first evolution has an second evolution in Gen2).

You can save them for that future evolutions (you can check those here), but you can just use them to power up your pokemon with some stardust as well.

I would say hold on to them, until Nintendo/Niantic releases Generation 2 Pokémon. I have some Scyther candy that I can't use, but I will be able to use them once they release Scizor, the evolved form of Scyther.

If you want, you can use them to power up your Pokémon, for example, Scyther or Taurus.

Keep the highest two or three CP Taurus and similar un-evolvable type mon you have. Free up storage space by transferring the rest to the professor. There are no negatives to holding the unusable (for now) candies.