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 (
    98260, 98259, 98258, 98257, 98256, 98255, 
    98254, 98253, 98252, 98251, 98250, 
    98249, 98248, 98247, 98246, 98245, 
    98244, 98243, 98242, 98241
  ) 
  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 0.00071

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
98241 1.69000000
98242 1.69000000
98243 1.69000000
98244 1.69000000
98245 1.69000000
98246 1.69000000
98247 1.69000000
98248 1.69000000
98249 1.69000000
98250 1.69000000
98251 1.69000000
98252 1.69000000
98253 1.69000000
98254 1.69000000
98255 1.69000000
98256 1.69000000
98257 1.69000000
98258 1.69000000
98259 1.69000000
98260 1.69000000