No, the empty potion bottles are not used for anything at all. At times, Morul will give you some of them( I presume because he ran out of time in terms of roleplay ;) ).

i remember when i used to play Dungeon Master Legends of Skull keep. ahhhhh, when i was yé hi, neways if u gave ur empty bottles to ur wizard and he had create potion spell, u could make any potion u wanted, shame u cant do that now tho?

Well, in Throne of Bhaal thieves can have the "Potions" ability and can make potions. Also they can write scrolls. I take a few of them for my Swashbuckler at High Levels.