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 (
    99122, 99121, 99120, 99119, 99106, 99104, 
    99099, 99052, 98970, 98764, 98763, 
    98762, 98761, 98760, 98759, 98758, 
    98757, 98756, 98755, 98754
  ) 
  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 0.00060

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
98754 1.69000000
98755 1.69000000
98756 1.69000000
98757 1.69000000
98758 1.69000000
98759 1.69000000
98760 1.69000000
98761 1.69000000
98762 1.69000000
98763 1.69000000
98764 8.99000000
98970 1.69000000
99052 1.69000000
99099 1.69000000
99104 1.69000000
99106 1.69000000
99119 1.69000000
99120 1.69000000
99121 1.69000000
99122 1.69000000