IMO: Best way to collect is not to do it, or to really evaluate why you want to collect.
My game collection has been mostly static these past few years, as I got into PC (Steam) gaming, which is all digital downloads. And I don't have a good place to display the games I have, which makes it not very fun to buy old games. They just sit in random piles or disorganized on some shelf.
But, once my house is a little cleaner, I'd like to reduce my collection to a small number of games that I adore, and have nice shelves (or maybe shrines

for them. I really like Endless Ocean on the Wii - so I thought about getting JPN and EUR copies of the game to compliment my NA copy, plus maybe a sealed copy too. Notice how this serves very little practical purpose. Practical collecting is a fool's game, IMO. Companies are getting very good about re-releasing games. The good games that aren't available for a reasonable price are few and far between - EarthBound may be an expensive SNES cart but it's $10 on the Wii U.
For me, game collecting is about showing appreciation for genres, series, games, systems, and companies you like. And to me, there's more value in a small collection of things you're passionate about than a collection of 1000 games you don't even like playing. (Nobody is out there playing their copy of Stadium Events or The Flintstones: The Surprise at Dinosaur Peak.) Sometimes that appreciation can be shown through merchandise, posters, and fanart prints rather than the games themselves. I own the fan-made Mother 3 handbook because I think that's a cool game, and the book is cool too.
I hate how arbitrary collecting is. I don't like the waves that each generation goes through - once the people who were 10 years old when X system came out graduate college and have jobs of their own, the prices of the games on those old systems go up. Looks like N64 games have almost hit their (temporary?) peak, and my guess is GameCube will follow in a few years. Super Smash Bros. Melee on GameCube was the bestselling game on the system, with 7 million+ copies sold. Somehow it's worth over $50 used. EarthBound isn't a rare game either, but so few people are willing to sell their copies that the game is worth a lot.
They're all just plastic, cardboard, and paper. I'm pretty sure most of them won't be worth anything in 50 years, because future generations won't care. Our generation isn't going around shopping for trinkets from 1964. It's difficult to argue that something with 7 million identical copies is inherently valuable.