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 (
    38067, 38037, 38036, 38034, 38033, 38032, 
    38031, 38030, 38029, 38028, 38027, 
    38026, 38025, 38022, 38021, 38020, 
    38019, 38018, 38017, 38016, 38015, 
    38014, 38013, 38012, 38011, 38010, 
    38009, 38008, 38007, 38006, 38005, 
    38004, 38003, 38002, 38001, 38000, 
    37999, 37998, 37997, 37996, 37995, 
    37994, 37993, 37992, 37991, 37990, 
    37989, 40283, 38872, 38159, 79896, 
    38226, 38078, 38077, 38076, 37988, 
    37987, 37986, 38458, 38423, 38422, 
    38421, 38420, 38419, 38418, 38417, 
    38400, 38399, 38244, 38227, 38172, 
    37985, 40512, 38181, 38180, 40355, 
    38884, 38062, 38043, 38042
  ) 
  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 0.00096

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