Been doing a daily ride to and from work now for over a year in just about every type of weather. My kit advice, for what it's worth:
Mudguards are essential, forget about aesthetics, when it's tipping it down you'll be glad you're not getting soaked from the road as well as the sky.
I wouldn't bother with a 'waterproof' - it comes down to preference but personally I've tried pretty much every combination of fabric, from £££ eVent through to your cheapie boil-in-the-bag type. If you're doing any sort of mileage then you're going to get wet one way or another and if you're wearing a waterproof, you're going to get hot and sweaty too. I've found that a decent softshell is far more breathable and more importantly for me, dries quicker and stays warmer too. When i get to the station I have a 30-40 minute train journey on the way to work and there's nothing worse than standing in a sodden waterproof shivering. Unless it's absolutely throwing it down usually I'll wear a gilet and armwarmers rather than a jacket and stick the jacket on when I get to the station. The gilet is windproof at the front so keeps the wind-chill down and stops your torso getting soaked as well. I use a Gore gilet and a Rapha softshell and armwarmers.
Merino wool is your friend. Again - insulates fantastically and dries really quickly. It also doesn't smell! I got my baselayers cheap from uniqlo and they've lasted a hard winters riding and washing without shrinking or shredding.
Sealskin socks are great. I've got both waterproof boots and 'normal' road cycling shoes but find myself wearing the shoes 99% of the time. If it's raining on the morning ride it means soggy footwear and I hate putting my feet into wet boots to cycle home. I find the lightweight, fast draining shoes dry out much quicker during the work day than the boots. Sealskins mean that your feet stay pretty toasty-warm regardless. If you can't stretch to them then M&S do decent Merino wool socks for about £9 for 3 pairs that are pretty good value for money.
A large portion of my ride is on unlit country roads so I've got light overkill with a Maxx-D and Joystick on bars/helmet and a Red-eye rear light. I'm also going to get a couple of knogs as 'backup' that I'll run flashing too. You have to be careful not to blind other road users with some of the current batch of lights as 900+ lumens is very bright. If it's all about being seen rather than seeing then I'd go with a combination of the usual recommended units from Cateye / Blackburn / knog.
As far as luggage goes I've got an Ergon rucksack that I can't recommend highly enough and a Carradice Super-C saddlebag. The only thing with the carradice is that when it's really heavily laden you have to be careful when out of the saddle that you don't move the bike from side-to-side as you easily tip over 
I've got a rack and may try panniers this winter but usually I travel light so it's a little OTT - it's far easier to stick a pack lunch and toolkit etc into the Ergon and strap it tightly to your back - the pivot joint means that you forget it's there.
(Good grief, sorry for banging on, I'll stop now )
