It depends on the gear. While various assessory items (chords, stands, etc) may be marked up 100% or more over cost other technology driver items (keyboards, mixers. etc) may be marked up as little as 10%-20%.
A general rule of thumb may be to anticipate that the store is working on a 40%-60% mark-up with a general goal to achieve 15% margin. As an example, if something is listed at suggested retail $500 (almost no one pays suggested retail) and the asking price is $450 there is a good chance the cost is in the $250 - $350 range (again depending on what it is). Perhaps the store needs to make 20% putting the bottom price at $300 - $420. In this case is you can pay $400 you may be getting a good deal.
These are all very general estimates. A big box store like Guitar Center may bring in gear at a lower cost than the local "mom & pop store" due to purchasing power - accordingly, the big store has more room to negotiate. I've see small stores in small towns get "suggested retail" because they are the only game in town.
If you purchase gear often enough and are able to establish a relationship with a given sales rep you can expect more or a discount. Often establishing a relationship with the "manager" is a good idea, since they may have a little more freediom to lower a price.
If you don't buy enough gear to achieve that, then your best bet is to do your homework, compare prices with other retial and on-line stores and then ask your store to meet or beat.