For newer stuff from 7th-8th gen, I can find most cib stuff pretty easily at GS,Amazon, and retail, except for a very rare titles or DS/PSP handheld stuff. For older stuff, its either Goodwill, Ebay, or deals with other forum members.
The local game stores in my area used to be pretty decent for picking up common stuff a few years ago, but now most of them price over Ebay and one store in particular has most of their game with sun damaged covers on top of that so I don't really bother with that.
I've also gotten to the point where some of the games I get are resold to cover the cost of expenses, usually dupes of stuff I already have.
My collection, especially in the early days, leans pretty heavily on Nintendo games as well as exclusives (especially for the Gamecube and Wii). If a game is multiplat, I usually look for the best version as long as its reasonably priced compared to the other options out there. Usually, I look for stuff to be cib, but if there is a huge price difference between loose and complete, then I'll go for the loose copy. I don't count Steam games in my collection; only eshop stuff so far. Most of my stuff is stored in my game room seperate from the house seperated by system, while excess stuff is boxed up in the main house.