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 (
    40629, 79914, 40775, 40774, 40621, 40620, 
    40616, 40948, 40187, 40186, 40185, 
    40779, 40778, 40231, 40174, 79928, 
    40167, 40166, 40165, 40531, 40773, 
    40772, 40157, 40156, 40152, 40151, 
    40150, 40069, 40111, 40110, 40857, 
    40106, 40102, 40101, 40099, 40098, 
    40097, 40096, 40088, 40087, 40081, 
    40092, 40007, 40006, 40005, 39997, 
    39994, 39982, 39980, 39977, 39976, 
    39975, 39974, 39973, 39972, 39971, 
    39970, 39969, 39968, 39967, 39966, 
    39962, 39950, 79918, 40105, 39991, 
    39960, 39923, 39916, 39907, 39906, 
    91051, 91050, 91049, 91048, 91047, 
    91046, 91045, 91044, 91043
  ) 
  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 0.00185

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 9 160 Using where

Result

product_id price
39906 1.69000000
39907 1.69000000
39916 1.69000000
39923 1.69000000
39950 1.69000000
39960 1.69000000
39962 1.69000000
39966 1.69000000
39967 1.69000000
39968 1.69000000
39969 1.69000000
39970 1.69000000
39971 1.69000000
39972 1.69000000
39973 1.69000000
39974 1.69000000
39975 1.69000000
39976 1.69000000
39977 1.69000000
39980 1.69000000
39982 1.69000000
39991 1.69000000
39994 1.69000000
39997 1.69000000
40005 1.69000000
40006 1.69000000
40007 1.69000000
40069 1.69000000
40081 1.69000000
40087 1.69000000
40088 1.69000000
40092 1.69000000
40096 1.69000000
40097 1.69000000
40098 1.69000000
40099 1.69000000
40101 1.69000000
40102 1.69000000
40105 1.69000000
40106 1.69000000
40110 1.69000000
40111 1.69000000
40150 1.69000000
40151 1.69000000
40152 1.69000000
40156 1.69000000
40157 1.69000000
40165 1.69000000
40166 1.69000000
40167 1.69000000
40174 1.69000000
40185 1.69000000
40186 1.69000000
40187 1.69000000
40231 1.69000000
40531 1.69000000
40616 1.69000000
40620 1.69000000
40621 1.69000000
40629 1.69000000
40772 1.69000000
40773 1.69000000
40774 1.69000000
40775 1.69000000
40778 1.69000000
40779 1.69000000
40857 1.69000000
40948 1.69000000
79914 1.69000000
79918 1.69000000
79928 1.69000000
91043 1.69000000
91044 1.69000000
91045 1.69000000
91046 1.69000000
91047 1.69000000
91048 1.69000000
91049 1.69000000
91050 1.69000000
91051 1.69000000