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 (
    94625, 94624, 94623, 94622, 94621, 94620, 
    94619, 94618, 94617, 94616, 94615, 
    94614, 94613, 94612, 94611, 94610, 
    94609, 94608, 94607, 94606, 94605, 
    94604, 94603, 94602, 94601, 94600, 
    94599, 94598, 94597, 94596, 94595, 
    94594, 94593, 95222, 95221, 95220, 
    95219, 94863, 94862, 94697
  ) 
  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 0.00075

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