I use the TCGPlayer average price as the value of my collection for insurance purposes. [The high prices are often ridiculous.] That's what I would expect to pay if I had to buy my entire collection card by card. The TCGPlayer average is often very close to what you'll find on StarCityGames.com and other sites.
In my experience, most shops will give you 30-50% of a card's value. A typical collector may offer you up to 75% of the value. That, incidentally, is a common selling point for many cards on Ebay (around 75% the TCGPlayer average), though prices there vary. Some collectors might offer you more, if you have specific cards they have been chasing. If many of the money cards you have are in Standard, you might get less, since most of those will see a price drop when they rotate out. Caveat venditor.
As to pricing at shops, remember that many price cards as they are put on display, and infrequently adjust them again. So, if a shop picked up a Thundermaw Hellkite when they were going for $40+, they might still have it priced near $40 today (especially if they bought it for $20). The same thing often happens when cards go up in price, so sometimes you find a steal. I was in two different shops during the past week. One had Gideon Jura for less than $5, and one had him at $11. Caveat emptor.
Other shops may have buyers who work only one or two days a week, so prices will get updated when they are working if they have time or are aware of significant price changes.