I'm a Nikon shooter so I'll vote for a Nikon
The D90 is a good high-end body that sits just below the professional lines and I'd suggest one of these if you plan on getting serious. The Nikon kit lenses are pretty good so with any Nikon grab the body+lens kit.
Probably the first thing to get would be a fast normal prime lens. On the consumer bodies a normal lens is below the 'conventional' 50mm -- so, go for the new Nikon AF-S 35/1.8.
For a flash an SB-600 will give you plenty of power and control. An alternative would be to initially go for a more compact 'mini'-flash such as the SB-400. ... less power and control but easily fits in pretty much any pocket.
Bags: Two I like are LowePro Mini Trekker AW backpack and the LowePro Rezo 180AW shoulder bag. Both would give you room to grow your kit. There is a Micro trekker backpack, smaller and still ok for a D90 though it doesn't have the all weather (AW) cover.
Tripods -- I'd go for a Manfrotto 190XPROB Pro Tripod and a good quality ball head.
I'd maybe wait on the tripod until you can afford an Arca-Swiss type ball head (e.g. a Markins Q3), they are expensive (~£260) but far, far better than anything else -- a joy to use. You will need a plate for your camera that slots onto the type of ball head you pick (~£40).
Other things to look at: a good circular polarizer, a rocket blower, a lens pen, an OpTech camera strap.