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 (
    125591, 122624, 125349, 113297, 122609, 
    122620, 125406, 122622, 122626, 109424
  ) 
  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 0.00064

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 20 Using where

Result

product_id price
109424 1.69000000
113297 1.69000000
122609 1.69000000
122620 1.69000000
122622 1.69000000
122624 1.69000000
122626 1.69000000
125349 1.69000000
125406 1.69000000
125591 8.99000000