The black-box version is the original, with 150 Pokemon. The red-box version is the "updated" Gold/Silver version, released when Pokemon Gold/Silver came out and the number of Pokemon increased from 150 to 250. If I remember right, they're essentially the same game, just more Pokemon in the red one.
A lot of merch from that Gold/Silver era, including this game, is pretty rare and sought after, I think *because* a lot of it was essentially the same game/thing as the original, so a lot of people that already had the original ones didn't get the G/S versions.
I'm not personally too "up" on the current values of Pokemon stuff, but looking on eBay sold items right now, I see one listed as 99% complete that went for $200. And there's one currently active with three days left and a bid for $145. If yours is only missing that one piece, I'd say it's definitely worth somewhere in the $150 - $200 range, if not more.