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 (
    95382, 95381, 95380, 95379, 95378, 95377, 
    95376, 95375, 95374, 95373, 95372, 
    95371, 95370, 94476, 94424, 94423, 
    94422, 94421, 94420, 94419, 94418, 
    94417, 94416, 94415, 94414, 94413, 
    94568, 94567, 94566, 94565, 94350, 
    94349, 94348, 94347, 94346, 94345, 
    94344, 94343, 94342, 94341
  ) 
  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 0.00049

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