What is the cheapest way to collect clone trooper minifigs?
I would say BrickLink... But it depends on how nitpicky you are, and what types of troopers you want. For example, if you're not trying to be ultra-canon with the Star Wars universe, you can just find the cheapest version of the Clone Trooper on BrickLink, and I'm sure you can find a decent price in a large quantity from a store. 

Other than that, I would suggest Craigslist. Craigslist can be iffy, but if you live in a well populated area, it can be a great resource (provided you are cautious, of course). If you buy from people who are just trying to 'get rid of all this lego' you can usually get things for cheaper. Try not to buy from people who know what they talking about, because they are collectors and are trying to make a high profit.

To sum things up, your best bet is BrickLink. If you're not a stickler, I'm sure there are some ways to slightly reduce the cost. 

Here's a good place to start:
92 New Clone Troopers 3.99 ea Definitely do some poking around, but this is one of the cheapest I could find if you want to buy large quantity of clone troopers. Obviously items that are 'used' will be cheaper, but the older troopers are more expensive, so the majority of cheap clones will be new. 

I know this response was a bit rambly, so please let me know if there's anything I can clarify.