The easiest answer is to know what to buy, the week they come out and buy them from your local comic book store at cover price. If you have multiple LCS’s within driving distance, scout them for how they price their comics. Regular covered comics should always be priced the cover price the week they come out. Some LCS’s will realize the value of the comic has risen, so they charge more for the price of the comic. If your LCS does that, find a new store. If the LCS didn’t buy enough of the issue to meet the demand, that’s on them and the consumer shouldn’t have to pay more for their mismanagement.
Variant covers are becoming more and more common among publishers to sell multiple copies of the same issue to collectors. Because variant commons tend to be rarer or have special artists doing the cover or unique features, stores often will charge more for the comic than their cover price. This is normal. How much more they charge depends on the store, which is what you need to determine. Many don’t charge extra for variants unless they’re issues that are more valuable. Most LCS’s charge $1 more for variants unless they’re more valuable and price higher based on market price. Then there are those who’ll charge significantly more for variants than market price. And finally, there are those LCS’s that rarely ever carry variant covers. So figure out what criteria the LCS’s in your area are and shop accordingly.
LCS’s typically carry older, rarer, or other valuable key issues that may catch your eye. Understand that LCS’s tend to charge more for these issues than on open market. EBay has many sellers competing with one another to make a sale, which brings the price of the issue down, while your LCS likely doesn’t have much competition for that one key issue in the area. Also, understand that your LCS’s ROI on that issue probably isn’t great as it is, as they were likely sold the issue at a fairly high price by the seller, but the store wanted it in the store in the same way a museum collects fine art; to draw people in to look, and if someone caves and buys it, they made their profit. You can always haggle with the shop for a lower price, or pay the difference to support your LCS. I see on Facebook groups all the time people taking pictures and throwing their LCS under the bus for overcharging these issues. While sometimes the difference in price is outrageous, that’s the store’s issue. Also, sometimes comics have hard-to-see autographs or other features that make the comic more valuable that you didn’t catch, so smearing their name across the internet is unfair to the store. Water always finds its level and it doesn’t need help doing so.
Comic Cons are typically a good way of getting a somewhat decent deal on comics. While sellers at cons typically know the value of what they’re selling, they’re also competing for sales with the seller next to them to make a sale. Sellers often offer a variety of deals, such as two-for-one sales and $1 issues, to draw buyers to their table, and then have their expensive items on display behind them. However, comic cons are hit or miss. I’ve been to plenty of cons where I drove over an hour, paid my admission, only to have a few sellers without anything worth buying.