SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    39989, 39981, 39862, 40074, 39961, 39818, 
    39808, 39643, 39642, 39445, 39505, 
    39150, 39149, 39271, 39418, 39074, 
    39119, 38831, 38821, 38943
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00081

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id usergroup 9 40 Using where

Result

product_id price
38821 1.69000000
38831 1.69000000
38943 1.69000000
39074 1.69000000
39119 1.69000000
39149 1.69000000
39150 1.69000000
39271 1.69000000
39418 1.69000000
39445 1.69000000
39505 1.69000000
39642 1.69000000
39643 1.69000000
39808 1.69000000
39818 1.69000000
39862 1.69000000
39961 1.69000000
39981 1.69000000
39989 1.69000000
40074 1.69000000