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 (
    39037, 39033, 39028, 16065, 16030, 15873, 
    14556, 15818, 15707, 15625, 15692, 
    15689, 15688, 15340, 15531, 15288, 
    14901, 14869, 39048, 14806
  ) 
  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 0.00060

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
14556 1.69000000
14806 1.69000000
14869 1.69000000
14901 1.69000000
15288 1.69000000
15340 1.69000000
15531 1.69000000
15625 1.69000000
15688 1.69000000
15689 1.69000000
15692 1.69000000
15707 1.69000000
15818 1.69000000
15873 1.69000000
16030 1.69000000
16065 1.69000000
39028 1.69000000
39033 1.69000000
39037 1.69000000
39048 1.69000000