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 (
    9963, 381, 429, 9913, 9912, 10139, 9916, 
    9911, 10138, 10217, 10142, 10141
  ) 
  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 0.00045

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 product_id 3 12 Using index condition; Using where

Result

product_id price
381 326.020000
429 2000.000000
9911 630.000000
9912 270.000000
9913 340.000000
9916 315.000000
9963 868.000000
10138 2259.000000
10139 1756.000000
10141 2745.000000
10142 2503.000000
10217 3933.000000