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 (
    88095, 88094, 88093, 88092, 88091, 88090, 
    88089, 88088, 88087, 88086, 88082, 
    88081, 87851, 87731, 87730, 87729, 
    87728, 88625, 88624, 88623, 88039, 
    88532, 88531, 88530, 88406, 88405, 
    88404, 88403, 88402, 88401, 87762, 
    87678, 88629, 88628, 88627, 88626, 
    88575, 88574, 88573, 88149
  ) 
  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 0.00107

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 80 Using where

Result

product_id price
87678 1.69000000
87728 1.69000000
87729 1.69000000
87730 1.69000000
87731 1.69000000
87762 1.69000000
87851 1.69000000
88039 1.69000000
88081 1.69000000
88082 1.69000000
88086 1.69000000
88087 1.69000000
88088 1.69000000
88089 1.69000000
88090 1.69000000
88091 1.69000000
88092 1.69000000
88093 1.69000000
88094 1.69000000
88095 1.69000000
88149 1.69000000
88401 1.69000000
88402 1.69000000
88403 1.69000000
88404 1.69000000
88405 1.69000000
88406 1.69000000
88530 1.69000000
88531 1.69000000
88532 1.69000000
88573 1.69000000
88574 1.69000000
88575 1.69000000
88623 1.69000000
88624 1.69000000
88625 1.69000000
88626 1.69000000
88627 1.69000000
88628 1.69000000
88629 1.69000000