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 (
    125358, 125461, 125089, 125066, 125487, 
    124934, 125127, 124797, 124795, 124990, 
    124970, 124816, 125134, 125133, 125030, 
    124778, 124470, 124653, 124477, 124475, 
    124857, 124312, 124309, 124180, 124483, 
    124302, 124301, 124033, 124449, 124269
  ) 
  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 0.00078

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
124033 1.69000000
124180 1.69000000
124269 1.69000000
124301 1.69000000
124302 1.69000000
124309 1.69000000
124312 1.69000000
124449 1.69000000
124470 1.69000000
124475 1.69000000
124477 1.69000000
124483 1.69000000
124653 1.69000000
124778 1.69000000
124795 1.69000000
124797 1.69000000
124816 1.69000000
124857 1.69000000
124934 1.69000000
124970 1.69000000
124990 1.69000000
125030 1.69000000
125066 1.69000000
125089 1.69000000
125127 1.69000000
125133 1.69000000
125134 1.69000000
125358 1.69000000
125461 1.69000000
125487 1.69000000