Hang your tools on a pegboard wall to organize them, keep them in sight, make them easy to access and reduce some of the risk of rusting by keeping tools in the open air. Pegboard is for sale at hardware stores that deal in large building materials. You can fit it with a wide variety of hooks, enough to fit even handheld power tools, and hang it to the wall.
Buckets are a simple solution for getting organized if you've got a lot of tabletop space but not a lot of shelf or drawer space. Use buckets and other thick, plastic containers to store small hardware, sorted by type, or to store hand tools. If storing heavy metal tools, however, you may need something to weigh the bucket down so it doesn't tip over with the weight of the tools. Try filling the bottom couple inches of the container with sand or rocks before adding the tools.
If you have drawer space, or even lower shelf space, use drawer dividers as a means of organizing smaller tools. If you can't find large desk dividers or tool dividers, use a large kitchen drawer organizer. Buy one made of thick, flexible plastic that can withstand the wear and tear of having tools tossed into it.
If you can't store your tools in an area where they're easy to spot, you'll need a system for organizing hidden storage compartments, like drawers, tubs or tool caddies. Store your tools by size if space concerns mean you have to maximize the efficiency of your storage space. This way, you can cram the maximum number of small tools into tiny spaces while insuring that the storage is big enough for large tools.
When space concerns aren't an issue, organize the storage of your tools according to what the tools do. This way, you'll have an easy time finding the right tool for the job since you'll have a readily available choice of multiple, similar tools.