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 (
    14641, 14640, 14637, 14635, 14634, 14633, 
    14632, 14631, 14630, 14629, 14628, 
    14627, 14626, 14481, 14480, 14482, 
    24684, 24683, 14436, 14434, 14438, 
    14437, 14411, 16539, 14409, 14410, 
    14101, 14138, 14137, 31447, 31446, 
    31445, 31444, 31443, 31442, 31441, 
    31440, 31439, 31438, 31437
  ) 
  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 0.00113

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 80 Using where

Result

product_id price
14101 1.69000000
14137 1.69000000
14138 1.69000000
14409 1.69000000
14410 1.69000000
14411 1.69000000
14434 1.69000000
14436 1.69000000
14437 1.69000000
14438 1.69000000
14480 1.69000000
14481 1.69000000
14482 1.69000000
14626 1.69000000
14627 1.69000000
14628 1.69000000
14629 1.69000000
14630 1.69000000
14631 1.69000000
14632 1.69000000
14633 1.69000000
14634 1.69000000
14635 1.69000000
14637 1.69000000
14640 1.69000000
14641 1.69000000
16539 1.69000000
24683 1.69000000
24684 1.69000000
31437 1.69000000
31438 1.69000000
31439 1.69000000
31440 1.69000000
31441 1.69000000
31442 1.69000000
31443 1.69000000
31444 1.69000000
31445 1.69000000
31446 1.69000000
31447 1.69000000