most places have no idea how to price items so thats irrelevant. most collectors will pay MAYBE 5% more for the game if they are into collecting variants. however there are a few games that do in fact demand a longbox premium, its just because the games themselves are rare (in that packaging) and most importantly, GOOD. they are Doom and Resident Evil. thats it. everything else is pretty much the same. the games that are only available in longbox may cost more than the average game of the same rarity (but again, depends if it was good). i think SF Alpha or whichever SF game that was thats in longbox may be somewhat sought after, but again its a good game regardless and in demand.
there are no longbox grails.
as for personal preference? i like the longbox games, but tend to stay away. the cartboard and plastic long boxes are a pain to find in good condition (and generally irreparable) and the long jewel cases are a pain to find and replace. finding a new one to replace with will sometimes cost as much or more than the shitty longbox game to begin with. sports games on the ps1 are all worthless to begin with, aside from like hot shots golf lets say (or even maybe one of the coolboarders games that was fun... thats worth more than $0.50, i think 3 was the best heh) 2 xtreme was fun, i guess, back when it came out. sports games from the 32bit era really didnt age well. actually the 16bit "3d" sports games didnt either (i mean like nba live, not nba jam).