Why does 2000 VW Passat 1.8T lose power while accelerating sometimes?

Could be bad gas. I would also check your diverter valve ($35 part at the dealership, google search for instructions), it is commonly blown out after 40K miles. The basic problem is that it blows out and leaks boost back into the airbox. The part was updated later and that is what the dealer will have. Generally if it is leaking you will only have 2 pounds of boost instead of the normal 8 pounds, at 7hp per pound you could be down over 25hp from stock.

The dealership will try to sell you a fuel injection service that you probably don't need.