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 (
    104503, 104502, 104566, 104565, 104564, 
    104563, 105544, 104462, 105512, 105462, 
    105461, 105460, 104547, 105405, 105404, 
    105403, 105402, 105401, 105400, 105399
  ) 
  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 0.00084

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
104462 1.69000000
104502 1.69000000
104503 1.69000000
104547 1.69000000
104563 1.69000000
104564 1.69000000
104565 1.69000000
104566 1.69000000
105399 1.69000000
105400 1.69000000
105401 1.69000000
105402 1.69000000
105403 1.69000000
105404 1.69000000
105405 1.69000000
105460 1.69000000
105461 1.69000000
105462 1.69000000
105512 1.69000000
105544 1.69000000