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 (
    95076, 94797, 94796, 94795, 94794, 94793, 
    94791, 94790, 94789, 94788, 94787, 
    94786, 94785, 94784, 94783, 94782, 
    94781, 94780, 94779, 94778, 96126, 
    96125, 96124, 96123, 96122, 95224, 
    94769, 94768, 94767, 94765, 94764, 
    94763, 94762, 94761, 94754, 94753, 
    94746, 94745, 94744, 94743
  ) 
  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 0.00071

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