I hear Sai and Photoshop are good programs, though I can't say I've used them.

I stick to MS Paint, it's a reliable program and if you know what you're doing with quite a bit of effort you can color and re-line over your own work without a sophisticated program or software. Is this done in MS Paint? If it is, and if you don't want to pay for programs, I would suggest getting used to the bucket and squiggly line tools. The squiggly line tool (or any other type of line tool), if done right, can do wonders for your drawings.

I use Paint Tool SAI and it works perfectly :)

You can try that out if you want, it has layers, effects, different types of color wheels, and lots of other tools :)