Also, if you do not want to spend on any specialized fountain pen flush solution, diluted windex works very well. From the smell I am willing to bet that most fountain pen cleaning solutions are exactly that.
I use J. Herbin's flush, which doesn't mind being used over and over. I filled an old Lamy 30ml ink bottle with one, and flush my pens with the same "liquid". From what I feel, it has some soap, some other surfactants, which it doesn't react with the rubber and seals inside the converters and pistons. Alcohol eats them from my experience.
The bottle I have gained interesting properties. It's a green-turquoise hue, which becomes reddish if you shine strong light through it :)
But it cleans like it's never used, which is nice.
I generally "power flush" my pens with a syringe: Get a 50ml syringe, cut the sealed end of a cartridge, fill the syringe, mate the syringe, cartridge, pen, and push the water through. After a couple of times, the pen is thoroughly cleaned. Shake a couple of times, let it dry.
On the other hand, many (if not most) inks have some detergents in it, and keep your pen clean and clog free as long as you use them. Older inks used Solv-X which was more effective but deemed carcinogen and banned in modern inks.