Commuting - How to secure equipment?

I am a new bike commuter, and I am trying to solve some problems. The biggest one is being able to transport and secure equipment. I should be carrying tools, tube repair kit, pump, etc. Does anyone have a way to secure those things to the bike so they can be left there? I would prefer to not have to remove everything when I park the bike. I have noticed those lockable trunk boxes, but they seem extremely unpopular, and expensive. Does anyone have a better solution?

Thanks for your help,
Andrew

Keep it in your panniers or backpack.

I keep mine in a pannier or backpack that I always remove.
Carry minimal toolkit. The further you ride, the more tools you had better carry.
Use a short minipump for everyday riding, it just has to get you home.
Use a pannier (or other bag) with a quick-release clip-on system.

For real utility riding, it is usually better to bolt stuff to the bike rather than use quick-releases. QRs mean that everytime you lockup, you have to remove all the bits. Removing lights, seatpost, wheels etc can be a real pain if you do it more than once a day.

I got the cheapest and smallest tools I could, and put them in a seat wedge bag I leave on the bike. (Its not mounted under the seat, though, I put on on the seat stays behind the cargo rack). With this setup I have everything I need for most minor repairs, but if someone steals the bag I lose only about $20.

Consider a seat bag that has a quick release so you can quickly remove and replace the bag at your destination. Topeak, for one, makes them.

If you are making short stops in low crime areas, then don't bother removing all your stuff. Just leave it on the bike and go about your business.