Buying by the case is generally the best option, but you might want to also check the trading card sections of local Targets, Best Buys, etc. as the remaining stock of SWM is being heavily liquidated. Currently it's possible to find:

4.99 - CW, CW Starter
6.99 - RotS, A&E, LotF, KOTOR
7.49 - IE, 2007 starter
8.99 - JA, GaW
10.99 - UNH, FU

I am trying to put together a 'playable' collection; meaning that I am trying to get 2-4 of each Uncommon, and 4-6 of each common (and sometimes more based on playability). I am trying to get in the best situation I can so when a V-sets is released I have the majority of the 'new' figures.

I am trying to finish out the sets, also. Mostly because I am addicted to plastic crack ;). Also, I am trying to create a program that will store and print all of the stat cards for a particular group of minis (a squad). To finish all of the scans, I have to have at least 1 of every card, and since I was so close to finishing all of the sets, I figured I would just buy everything else that I needed.
I want to show off my collection, so here it is. ;)

Masters of the Force (40/40); 64 total
The Dark Times (40/40); 64 total
Galaxy at War (40/40); 64 total
The Crystal Caves of Ilum (2/2); 2 total
Jedi Academy (40/40); 64 total
Showdown at Teth Palace (2/2); 2 total
The Attack on Teth (2/2); 2 total
Imperial Entanglements (40/41); 65 total
Clone Wars Battles (10/10); 10 total
The Clone Wars Starter Set (6/6); 6 total
The Clone Wars (40/40); 65 total
Knights of the Old Republic (60/60); 93 total
Legacy of the Force (60/60); 92 total
The Force Unleashed (55/60); 85 total
Battle of Hoth (0/17); 0 total
Starter Set (6/6); 6 total
Rebels and Imperials (0/24); 0 total
Alliance and Empire (59/60); 93 total
Bounty Hunters (50/60); 73 total
Champions of the Force (60/60); 96 total
Attack on Endor (3/4); 3 total
AT-AT Imperial Walker (1/1); 1 total
Universe (53/60); 82 total
Revenge of the Sith (57/60); 91 total
Clone Strike (56/60); 89 total
Rebel Storm (55/60); 88 total

Good luck on finishing out your collection, as this is the perfect time to do it. A lot of people are selling complete sets on e-bay, and even if others are buying them, they will have tons of extras to trade and/or sell to you through this site or any other trading site.

If you were to pick up a couple cases worth of miniatures to trade and or finish your collection, I would agree with EmperorDragon and try to pick up as many 4.99 to 10.99 boosters from Target/Bestbuy/other and focus on trading. (For you, get as many clone wars/Kotor/Legacy as you can before they are out of the liquidated stock)

How the heck do you guys end up with so little of these sets? I have at least 300 IE minis. Most of them, I would kind of rather not have, unless the game evolves to the point where I want 35 Whiphid trackers in a squad. Do you buy mostly singles, somehow trade away the extra C/UC, just toss them in the trash? What's the secret here?

Most people just buy boosters in singles or occasionally buy a case for gifts like holidays. UP untill clone wars i didnt buy a single case. And those are the sets i need most of. My standings are currently
Masters of the Force (38/40); 78 total
The Dark Times (38/40); 85 total
Galaxy at War (40/40); 89 total
Jedi Academy (39/40); 98 total
Imperial Entanglements (40/41); 120 total
The Clone Wars (40/40); 104 total
Knights of the Old Republic (53/60); 109 total
Legacy of the Force (54/60); 146 total
The Force Unleashed (54/60); 87 total
Alliance and Empire (57/60); 96 total
Bounty Hunters (59/60); 106 total
Champions of the Force (57/60); 124 total
Universe (52/60); 104 total
Revenge of the Sith (50/60); 95 total
Clone Strike (51/60); 120 total
Rebel Storm (50/60); 144 total
You have 844/915 minis, and 1778 total. Your collection is 92.24% complete.

I just figured that out before coming to this thread.