check hcrealms.com
Also, before you buy anything check their Sell forums. Lots of guys selling off complete sets and singles far cheaper than cracking open boxes or buying from stores. I've gotten all my clix off other players there. I rarely buy boxes anymore.
link
Figures from 'drop box' sets will be more expensive per figure due to the small nature of the set. But figures from large 'buy it buy the brick' sets will be cheaper. I usually buy those sets for $35 USD shipped--often 40+ C/U/R figures plus maybe the brick figure and a map tossed in depending on who is selling. Ultra-rares will cost more of cost, but always seem to drop in price as new sets come out.
Take your time. Deals always come up.
Star Trek:
Not very popular among the clix players, so harder to get singles on hcrealms. Miniature Market sells the ships as singles cheaper than anyone, including my local store Cool Stuff. Common ships are cheap, rares are a bit more expensive to crazy-expensive. The problem with the game is that many guys complained that the ships had broken parts due to shipping. Problem is that you can't tell by looking at the blind boxes.
miniaturemarket.com
The ST: Attack Wing is coming very soon, re-using the clix ships but you will see them in open blisters. No blind buys. Downside is that the ships they are releasing sell online by MM and gamers as clix singles for only $1 USD or $2 USD, but now they will be $10 USD each. Upside is that the Enterprise will be $10 USD instead of $25 USD on the secondary market. Granted, the AW ships will have a new base and some game cards. But still, WK is using their crap stat ships in the release of the game. link