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 (
    88461, 88412, 88396, 89357, 89198, 88514, 
    88484, 88483, 88482, 88463, 88462, 
    89197, 89196, 89013, 89012, 89011, 
    88992, 88991, 88990, 88989, 88988, 
    88987, 88986, 88985, 88984, 88983, 
    88982, 88952, 88951, 88950, 88949, 
    88948, 88947, 88946, 88841, 88840, 
    88831, 88830, 88829, 88828
  ) 
  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 0.00106

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 80 Using where

Result

product_id price
88396 1.69000000
88412 1.69000000
88461 1.69000000
88462 1.69000000
88463 1.69000000
88482 1.69000000
88483 1.69000000
88484 1.69000000
88514 1.69000000
88828 1.69000000
88829 1.69000000
88830 1.69000000
88831 1.69000000
88840 1.69000000
88841 1.69000000
88946 1.69000000
88947 1.69000000
88948 1.69000000
88949 1.69000000
88950 1.69000000
88951 1.69000000
88952 1.69000000
88982 1.69000000
88983 1.69000000
88984 1.69000000
88985 1.69000000
88986 1.69000000
88987 1.69000000
88988 1.69000000
88989 1.69000000
88990 1.69000000
88991 1.69000000
88992 1.69000000
89011 1.69000000
89012 1.69000000
89013 1.69000000
89196 1.69000000
89197 1.69000000
89198 1.69000000
89357 1.69000000