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 (
    125139, 125138, 125136, 125123, 125652, 
    125492, 125025, 125024, 125020, 125568, 
    125566, 124982, 125496, 124870, 124859, 
    124858, 125412, 125411, 124963, 124733, 
    124731, 124573, 124546, 124358, 124737, 
    124650, 124299, 124231, 124217, 124215
  ) 
  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 0.00089

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 60 Using where

Result

product_id price
124215 1.69000000
124217 1.69000000
124231 1.69000000
124299 1.69000000
124358 1.69000000
124546 1.69000000
124573 1.69000000
124650 1.69000000
124731 1.69000000
124733 1.69000000
124737 1.69000000
124858 1.69000000
124859 1.69000000
124870 1.69000000
124963 1.69000000
124982 1.69000000
125020 1.69000000
125024 1.69000000
125025 1.69000000
125123 1.69000000
125136 1.69000000
125138 1.69000000
125139 1.69000000
125411 1.69000000
125412 1.69000000
125492 1.69000000
125496 1.69000000
125566 1.69000000
125568 1.69000000
125652 1.69000000