For general maintenance I'll use a warm water flush, just trickling the warer through the stummel with the stem removed, scrubbing it out with either shank brushes, wire bristle cleaners, q-tips for the mortise, and wiping the chamber with a wadded paper towel to remove recent cake. If the stem is vulcanite, it gets cleaned with a few passes of pipe cleaners that have been lightly soaked in alcohol, making sure to thoroughly clean out the funnel and the slot. If the stem is acrylic I use a few damp pipe cleaners that have been dipped in unscented dishwasher gel to scrub out the acrylic. No water on vulcanite and no alcohol on acrylic. That does an excellent job for regular maintenance.
But recently I've been doing a heavy duty cleaning job to neutralize a number of my more heavily used pipes where normal maintenance didn't quite get rid of the sour note. With these it's alcohol all the way, many scrubings until the pipe cleaner is barely pulling even the littlest bit of color. Then I just barely dampen the bristle pipe cleaner, work it back and forth in the airway, and leave it in, hanging the pipe off the edge of my workbench with the shank hanging down, and let it dry overnight to pull any stubborn oils out of the wood. I'll repeat this on successive days with fluffies that have been barely moistened with alcohol, hanging the pipes shank down, and let them pull any remaining oils out of the airway as the pipe cleaner dries out. The mortise gets the same treatment, sucking out any stubborn oil deposits until it's not just wood, but clean wood. I'll also sand back the cake until it's just a thin veil. It's the routine I would use on neutralizing an estate, or readying a pipe for sale.
After the intensive cleaning, the water flush treatment does a great job of keeping the pipe fresh.