In Red/Blue/Green/Yellow, FireRed/LeafGreen, and Black/White, it is impossible to get multiple Master Balls legitimately. Aside from the one time methods that generally happen during the main storyline, you can get more Master Balls from the in-game lottery.
G/S/C:
>Goldenrod Radio Tower (match all 5 digits in the Lucky Channel)
R/S/E:
>Lilycove Department Store (match all 5 digits in the Pokémon Lottery Corner)
D/P/Pt:
>Jubilife TV (match all 5 digits in the Pokémon Lottery Corner)
HG/SS:
>Goldenrod Radio Tower (match all 5 digits in the Lucky Channel)
B2/W2:
>Join Avenue (grand prize from Raffle Shops)
X/Y:
>Loto-ID Center (match all 5 digits)
OR/AS:
>Pokémon Lottery Corner (match all 5 digits)
S/M, US/UM:
>Loto-ID Center (match 5 digits), Festival Plaza (Lottery shop: Big Dreams first prize)
LGP/E:
>Cerulean Cave
Sw/Sh
>Any Pokémon Center (match all 5 digits in the Loto-ID)
You can also get a second master ball in Black/White from a man in the Castelia City Pokemon Center, after you've obtained Pokemon with 50 different OTs. Furthermore, Master Balls can also be obtained through event distributions. A list of those is included in the source below.
Source