Shortest Longest Increasing Subsequence Code
Python 3, 66

Note that all numbers are in range [1, 999], we can use an array b to maintain the longest subsequence length ending with each number. b[x] = d means that the longest subsequence ending with x has length d. For each number from the input, we update the array using b[x] = max(b[:x]) + 1 and then we got the job done by taking max(b) finally.

The time complexity is O(n) O(m n), where m is always 1000 and n is the number of input elements.

def f(a):
 b=[0]*1000
 for x in a:b[x]=max(b[:x])+1
 return max(b)


Wow, looks like already ungolfed :)
You can test it using stdin/stdout by adding a line:

print(f(map(int,input().split())))