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 (
    106065, 106064, 106063, 106062, 106060, 
    106059, 106058, 106057, 106056, 106055, 
    106054, 106053, 105009, 105008, 105007, 
    105006, 105005, 105004, 105003, 106207
  ) 
  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 0.00047

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
105003 1.69000000
105004 1.69000000
105005 1.69000000
105006 1.69000000
105007 1.69000000
105008 1.69000000
105009 1.69000000
106053 1.69000000
106054 1.69000000
106055 1.69000000
106056 1.69000000
106057 1.69000000
106058 1.69000000
106059 1.69000000
106060 1.69000000
106062 1.69000000
106063 1.69000000
106064 1.69000000
106065 1.69000000
106207 1.69000000