SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    95595, 95594, 95593, 95592, 95591, 95590, 
    95589, 95588, 95587, 95586, 95585, 
    95584, 95583, 95582, 95581, 95580, 
    95579, 95578, 95577, 95576, 95575, 
    95574, 95573, 95572, 95571, 94905, 
    95440, 95439, 94679, 94678, 94677, 
    94676, 94675, 94674, 94673, 94672, 
    94659, 94629, 94628, 94626
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00057

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_ult_product_prices range usergroup,product_id,company_id,lower_limit,usergroup_id usergroup 13 1 Using where