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 (
    94742, 94741, 94740, 94739, 94738, 94737, 
    94736, 94735, 94734, 94733, 94732, 
    94731, 94730, 94729, 94728, 94727, 
    95619, 95618, 95617, 95616, 95615, 
    95614, 95613, 95612, 95611, 95610, 
    95609, 95608, 95607, 95606, 95605, 
    95604, 95603, 95602, 95601, 95600, 
    95599, 95598, 95597, 95596
  ) 
  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 0.00060

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