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 (
    3316, 8888, 1310, 9821, 9965, 8877, 9823, 
    721, 10066, 10095, 1311, 10013
  ) 
  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 0.00083

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
721 199.000000
1310 378.380000
1311 2.000000
3316 0.000000
8877 2925.000000
8888 2449.000000
9821 1316.000000
9823 1617.000000
9965 799.000000
10013 1899.000000
10066 274.800000
10095 0.000000