What is the smallest integer with 100 non trivial factors? Excluding 1 and itself as factors, what is the smallest integer with 100 different factor values? 

Example: 20 has 4 non trivial factors (2*10 and 4*5)
Assuming you mean "exactly $100$ non-trivial divisors".

If the natural number $n&gt;1$ has prime decomposition $n=\prod p_i^{a_i}$, the total number of factors is $$d(n)=\prod (a_i+1)$$  

As you wish to exclude $1$ and $n$, you are interested in $F(n)=d(n)-2$.  We see that you are requiring $F(n)=100$ or, equivalently, $d(n)=102$

Now, $102=2\times 3\times 17$.  We therefore seek $\{a_i\}$ with $\prod (a_i+1)=2\times 3\times 17$.  We remark that our $n$ can not have more than three prime divisors.

Case I:  One prime.  Then the best we can do is $n=2^{101}$ which seems unlikely to be minimal.

Case II.  Two primes  Then the best we can do is $2^{16}3^5$, certainly a lot better than $2^{101}$

Case III. Three primes.  Now the best we can do is $2^{16}3^25$, which is only $\boxed {2949120}$.
If it has to be 100 different prime factors, the 10 year olds in my class looked at the pattern of answers starting at 1 prime factor, 2,3,4, 5,6 etc and the size of the numbers (powers of $10$). We decided that as a minimum the answer must have at least $98$ zeros.