SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    98376, 98365, 98364, 98362, 98353, 98226, 
    98177, 97708, 97684, 97679, 97678, 
    97664, 98178, 98267, 98266, 98265, 
    98264, 98263, 98262, 98261
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00050

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id usergroup 9 40 Using where

Result

product_id price
97664 1.69000000
97678 1.69000000
97679 1.69000000
97684 1.69000000
97708 1.69000000
98177 1.69000000
98178 1.69000000
98226 1.69000000
98261 1.69000000
98262 1.69000000
98263 1.69000000
98264 1.69000000
98265 1.69000000
98266 1.69000000
98267 1.69000000
98353 1.69000000
98362 1.69000000
98364 1.69000000
98365 1.69000000
98376 1.69000000