The Topeak kit is an OK deal; I think it's about the same as buying the parts individually. Thing is, by going individual, you get more customization if you want different brands of stuff.

Given that you already have a couple of the components in the kit, I think you can save a little money by getting individual parts.

Pedro's multi-tool: http://www.amazon.com/Pedros-Folding...dp/B000IZEH9C/
I like that one because it has screwdrivers; can't believe other multi-tools leave those out while including random stuff you'll never use. Some people go apecrap carrying stuff like chain tools and spoke wrenches, but for your average joe, I think that one will serve well.

Pocket Rocket mini pump: http://www.amazon.com/Topeak-Pocket-...dp/B000FI6XGC/
Popular, serviceable, cheap. Others will prefer other, more expensive mini pumps, but I don't think anyone will argue you got a lemon with that one.

If you're a commuter, I suggest you think hard about getting some tires with major flat resistance. A tire like Marathon Plus is almost bombproof and has awesome longevity. They can be a ***** to get on, but IMO the money spent is well worth the peace of mind, durability, and convenience of not having to mess around changing a flat at a bad time. (Really, is there ever a good time to change a flat?)