I prefer having the case and manual, but I have bought loose games before just so I could have them. I bought Prince of Persia: Sands of Time on PS2 after sifting through a box of loose games at Gamestop when I was a kid. The only reason I bought it was because the disc had cool art. I became a huge PoP fan after playing that game, so I don't ever regret buying it without a case. After my PS2 stopped working when I tried some stupid self repair, I rebought SoT on Gamecube and I got it with a box and I was very happy.
Sometimes I used to buy retro games that came with correct manuals and the proper box art, but the case was just for a DVD. When that would happen I'd put a game I didn't like as much in the DVD case and the game in the correct casing and then swap the box art and manuals.
I've been considering buying proper cases for the games I have that are missing them. Maybe the manuals for the case too but I think that can get expensive? As for the box art, I've considered getting the correct printing paper that they use for box art because I know there are websites that have the correct image specifications for the box art so you can use a printer to make your own.