+1 vote for ebay. As well as for making organizers oneself.
Also I try to do as much price comparison before purchase as I can (say, if Im looking for particular kit Ill try nearest off-line shops, on line stores and the site of a kit manufacturer, and the last sometimes is the cheapest option even taking postage prices into account). Sometimes subscribing to e-mail subscriptions of retailers and manufacturers may be helpful - theyll let you know about sales and promotions. Stitching technology is also important: I try to save as much floss as possible, less lose ends and so on. And socializing, too - having friends with the same hobby is really great)
I shop at secondhand stores for many of my crafting supplies. Locally they sell hoops for $0.10-0.50 depending on size. Needles and floss often in a bag labeled "assorted embroidery" and my fabrics and many patterns come from there. Just walk in and ask where their crafting stuff is.
I try to wait for the 30% off or more total sale items coupons from craft stores. A couple of times a year, your regular and sale price items will be discounted and extra 20 to 30% of total purchase. Thats when I buy 2 sets of every DMC color they have! I can stitch for as long as I can see! :D
I shop on ebay for bundles of threads - there are lots of sellers who sell 50 or 100 skeins for a set price, and you give them a list of the colors you need.
I bought boxes to hold my bobbins from the hardware store - theyre made for holding screws and nails, and use scrap cardstock to make my own bobbins.
I make my own pako needle organizer by using a sponge with strips of paper with the symbols drawn on them.
I use a hole punch and print off my own thread organizers for each pattern I am working on and cut 1 - 2 lengths of floss at the length I work with (usually just 12" since I stitch on 28 count in heavy confetti patterns) and store those in a plastic sleeve with my pattern so that I dont have to keep messing with my bobbins all the time.
I buy needles in bulk (packs of 50 needles for about $10) so that I dont have to pay full price. I store them in altoid tins with a magnet in each tin so that the needles dont go flying when I open the tin.
I bought cuticle scissors to use instead of expensive embroidery scissors at the craft store - a great pair cost only about $4 and work just as well.
Use a cool color lightbulb in a gooseneck lamp that I can adjust instead of buying an expensive replacement bulb for my ott light. 3 light bulbs only cost me $6 at walmart and I have been using it 2 - 5 hours a day every day for 6 months and the first one is still going strong.
I also make sure I use coupons to buy my fabric - joanns and micheals have coupons nearly every week. I also dont buy stash just to have it. I have no more than 2 items on the go, and fabric for the next project I want to start ready so when I finish one I can start the next without having to go shopping.