The sequence $a_1, a_2, \ldots$ is geometric with $a_1=a$ and common ratio $r,$ where $a$ and $r$ are positive integers. Given that $\log_8 a_1+\log_8 a_2+\cdots+\log_8 a_{12} = 2006,$ find the number of possible ordered pairs $(a,r).$

\[\log_8 a_1+\log_8 a_2+\ldots+\log_8 a_{12}= \log_8 a+\log_8 (ar)+\ldots+\log_8 (ar^{11}) \\ = \log_8(a\cdot ar\cdot ar^2\cdot \cdots \cdot ar^{11}) = \log_8  (a^{12}r^{66})\]
So our question is equivalent to solving $\log_8 (a^{12}r^{66})=2006$ for $a, r$ positive integers. $a^{12}r^{66}=8^{2006} = (2^3)^{2006} = (2^6)^{1003}$ so $a^{2}r^{11}=2^{1003}$.
The product of $a^2$ and $r^{11}$ is a power of 2. Since both numbers have to be integers, this means that $a$ and $r$ are themselves powers of 2. Now, let $a=2^x$ and $r=2^y$:
\begin{eqnarray*}(2^x)^2\cdot(2^y)^{11}&=&2^{1003}\\ 2^{2x}\cdot 2^{11y}&=&2^{1003}\\ 2x+11y&=&1003\\ y&=&\frac{1003-2x}{11} \end{eqnarray*}
For $y$ to be an integer, the numerator must be divisible by $11$. This occurs when $x=1$ because $1001=91*11$. Because only even integers are being subtracted from $1003$, the numerator never equals an even multiple of $11$. Therefore, the numerator takes on the value of every odd multiple of $11$ from $11$ to $1001$. Since the odd multiples are separated by a distance of $22$, the number of ordered pairs that work is $1 + \frac{1001-11}{22}=1 + \frac{990}{22}=46$. (We must add 1 because both endpoints are being included.) So the answer is $\boxed{46}$.
For the step above, you may also simply do $1001/11 + 1 = 91 + 1 = 92$ to find how many multiples of $11$ there are in between $11$ and $1001$. Then, divide $92/2$ = $\boxed{46}$ to find only the odd solutions.