I agree with Cdryden about knowing what you want and being patient. I've overpaid a couple times because I found my "perfect" cue but the guy wouldn't budge on price...only to have another "perfect" cue at a better price become available a month later.
Retail on production cues is a mythical price that no one pays so that everyone can claim to have it on sale. Example: a Schon stl-1 (a great cue, btw). Retail is $595, but just try to find one that isn't listed for $475/476 or so. (that's 20% off, btw, the max places are allowed to discount).
You can haggle and some places will hook you up with a little more of a discount, but that's kinda hush hush

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For custom cues, retail is the maker's starting asking price. They can ask whatever they want so to some degree you can haggle, but you will usually pay close to what they originally ask. Their attitude (which I understand, and completely respect) is essentially, "I made this cue, this is what I want for it."
Contrary to popular belief, custom cues usually lose value on the secondary market. Not normally as bad as production cues, but I'm willing to bet 90%+ of custom cues' highest sale price is their initial sale price. Sometimes a maker jumps into the stratosphere of desirability for whatever reason and their cue values soar (Southwest, for example, Sugartree more recently, although the market for those has been declining a bit) and you can make money. But as a general rule I would treat buying a custom cue like buying a car: you lose 20% the moment you take it off the lot, so to speak.