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 (
    41027, 41026, 41025, 41024, 41023, 41022, 
    41021, 41020, 41019, 41018, 40998, 
    40954, 40896, 40895, 40894, 40888, 
    41357, 41356, 41355, 41354, 41353, 
    41352, 41351, 41350, 41349, 41348, 
    41347, 41346, 41345, 41344, 41343, 
    41342, 41341, 41340, 41338, 41337, 
    41336, 41335, 41334, 41333, 41332, 
    41331, 41330, 41329, 41328, 41327, 
    41326, 41325, 41324, 41140, 40854, 
    40853, 41004, 41003, 41002, 40946, 
    40842, 40841, 40837, 40836, 40835, 
    40834, 40833, 40872, 40866, 41147, 
    40784, 40783, 40777, 40776, 40798, 
    40797, 40686, 40671, 79898, 40781, 
    40780, 40642, 41150, 40634
  ) 
  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 0.00189

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 9 160 Using where

Result

product_id price
40634 1.69000000
40642 1.69000000
40671 1.69000000
40686 1.69000000
40776 1.69000000
40777 1.69000000
40780 1.69000000
40781 1.69000000
40783 1.69000000
40784 1.69000000
40797 1.69000000
40798 1.69000000
40833 1.69000000
40834 1.69000000
40835 1.69000000
40836 1.69000000
40837 1.69000000
40841 1.69000000
40842 1.69000000
40853 1.69000000
40854 1.69000000
40866 1.69000000
40872 1.69000000
40888 1.69000000
40894 1.69000000
40895 1.69000000
40896 1.69000000
40946 1.69000000
40954 1.69000000
40998 1.69000000
41002 1.69000000
41003 1.69000000
41004 1.69000000
41018 1.69000000
41019 1.69000000
41020 1.69000000
41021 1.69000000
41022 1.69000000
41023 1.69000000
41024 1.69000000
41025 1.69000000
41026 1.69000000
41027 1.69000000
41140 1.69000000
41147 1.69000000
41150 1.69000000
41324 1.69000000
41325 1.69000000
41326 1.69000000
41327 1.69000000
41328 1.69000000
41329 1.69000000
41330 1.69000000
41331 1.69000000
41332 1.69000000
41333 1.69000000
41334 1.69000000
41335 1.69000000
41336 1.69000000
41337 1.69000000
41338 1.69000000
41340 1.69000000
41341 1.69000000
41342 1.69000000
41343 1.69000000
41344 1.69000000
41345 1.69000000
41346 1.69000000
41347 1.69000000
41348 1.69000000
41349 1.69000000
41350 1.69000000
41351 1.69000000
41352 1.69000000
41353 1.69000000
41354 1.69000000
41355 1.69000000
41356 1.69000000
41357 1.69000000
79898 1.69000000