I just asked the same question earlier this week, after deciding to resurrect two pens of mine that had 20 year old ink in them.
I soaked them in lukewarm water, and then flushed them out with lots of cold water. Just plain water worked fine for me, although it took a lot of rinses to get all the ink out. I let them dry overnight, put fresh ink in today and they worked fine.
I put a little bit of ammonia in cool water. I let the working parts sit in the solution for a few hours, and then flush. once the pen starts only squirting out clean solution I flush well with clean water, and then let the pen sit open with the nib in bunched up tissue to wick out the water for a day or so. Seems to work well enough most of the time.
Before you put them in an ammonia solution, let us know what kind of pens they are and some pics would help. Some pens should not be put in an ammonia soultion.
It will be helpful to know what kind they are and how old. Even soaking too long in water can discolor or damage some really old pens. Depending on the filling mechanism they may require a little work to get them going again, but it is well worth the effort.
While we're on the subject of ammonia and cleaning - can ammonia be used on the inside of the Parker Vacumatics, to clean the inside of the barrel? Or is that a big no-no? And what are the other things that ammonia can damage?
Before I do the ammonia soak I use a drop of dish detergent in a bowl of cool water to flush the pen and then let it soak for a few hours. If there's still ink coming out when I flush it after that time I do another round. I tend to use ammonia only for the most stubborn of stains.
Does the nib unit come out? If so you could try cleaning with a tiny bottle brush and some ammonia/water solution. The overall bluish tint was common for many German piston fillers (Geha, Pelikan, Montblanc) or is there a particular stain you're seeing -- I'm not.