As someone who sells bike bags for a living... I have a great little front rack bag by Zimbale that carries my tools, tube, phone, wallet and I can even stuff my jacket in. For round town I have a metal basket Zipped Tied to my rear rack love it, I have one of those cool spider bungee nets - they are pretty inexpensive. I simply remove the basket when I go on a trip that I need my panniers - I like the Racktime's
I have two friends who use the topeak system on their commuters, one has the rear rack with the trunk bag and the other has the same rack but with the snap on basket and the same bungee net I use. Both have been super happy with them.
Of course, when we have a big shopping trip planned we cheat and take the bob trailer but most of the time I can get by with my basket and top rack bag.