+1 on the multi-tool, tube, and patch kit. They can fit easily into most seat bags; I use this one. The "Twistlock" allows me to easily transfer it from bike to bike. There are as many choices for pumps out there as there are for bikes. Some prefer CO2 inflators for their small size and convenience but I am comfortable with my pump, which attaches nicely to either of my 700c commuters:




As for keeping things dry I rely on my pannier; it's water-resistant enough to stand up to anything short of a deluge, but for really wet days I purchased the optional raincover. Arkel panniers aren't cheap, but like many things bike-related, you get what you pay for. I've had the bag for almost 3 years, riding through all kinds of conditions, and it still looks and works like new.