Following are few the bots still active:
Pokecrot: Pokecrot is more advance and has easy to understand UI to use. Pokecrot is actively updated. So do check our for latest versions.
NecRobot: NecRobot is one of the oldest Bots. Its has simple command prompt base UI. Its is maintained by community.
Both this bots are open sourced so you can have look at the code too. There are few other paid bots (like mygobot), but who needs paid app when you can get one for free ;).
We do not encourage using bots as it kills the fun of playing game as it should be. Still do let me know if you are using any other bots and your valuable feedback of the same.