How to summon potions on the ground in minecraft 1.9
The Damage tag no longer holds the type of default potion. Instead, the Potion string within the tag compound states the name ID of the default potion.
As well, you should not be using numerical IDs for items since 1.8 and should have instead been using name IDs. In 1.9, numerical IDs are no longer used.
/summon Item 343 5 -641 {Item:{id:"minecraft:potion",Count:1b,tag:{Potion:"minecraft:healing"}}}
The wiki lists different potion IDs here.