SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    10011, 9933, 10121, 9852, 10364, 725, 
    10389, 8376, 10069, 10122
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 3 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00048

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_ult_product_prices range usergroup,product_id,company_id,lower_limit,usergroup_id usergroup 13 20 Using index condition

Result

product_id price
725 1034.000000
8376 45.000000
9852 571.000000
9933 939.000000
10011 0.000000
10069 110.000000
10121 90.000000
10122 45.000000
10364 176.440000
10389 95.000000