For the sake of good recommendations it'd be helpful to know what car you have and what it's purpose is... primarily spirited DD? Will it see frequent track use?
A track pad or at least a street performance pad would be the first thing to consider. Some criteria to consider are the pad material, metallic or ceramic mainly. Metallic dust more but are cheaper and good ones have just as much or more stopping power as ceramic and consistent bite when hot or cold. Ceramic barely dust but bite is inconsistent as they work best when they are hot, they also don't tend to bite as well as top-tier metallics in my experience but everyone seems to have a different opinion on that and it probably just comes down to the quality for the most part. A lot of people assume they bite more because they are on high end cars... not necessarily. Also look into their temp range, in other words how much they can handle before you get brake fade. These days I'm just using StopTech sport pads since I have a StopTech big brake kit on my front end. I'm impressed with the pads and would have no issue recommending them. I can also recommend Hawk HPS 5.0 or EBC pads (green, yellow, or red series, depending on your preference/application). The EBC pads I've run stop damn well and seem to never fade but they are a bitch to bed in properly, are noisy for quite awhile, and aren't super consistent in my experience. Also, contrary to how they are advertised, they are notoriously harsh on rotors, which incidentally is another criteria to consider with the pads you choose. There are plenty of other options out there too. It's up to you.
As for rotor type... this is a hugely overblown subject. The reality is the type of rotor you choose, whether it be blank, slotted, drilled, whatever, makes veeery little difference for performance. I'd get blank or slotted, NO drilled. Drilled is an aesthetic thing only no matter how much every company trumpets the claim that they are for better heat dispersion, etc. The fact is drilled rotors are just for looks and the only thing you're gonna get with them is a greater risk of heat cracking your rotor because its structural integrity with all those holes is weaker. Not saying its likely at all on a street car, just saying its more likely. So unless you really just love the look of drilled rotors then stay away. The same marketing claims about slotted rotors when it comes to the difference they make because of heat/gas dispersion is mostly hocus pocus too but at least slots don't sacrifice structural integrity. I also like the way slotted rotors look (unlike drilled which I think look ugly) so I'd go for slotted. They can shave your pads down a little faster though. Two-piece vs. one-piece isn't a huge matter either; yes, two-piece will be lighter which reduces unsprung weight and can have a tangible affect on acceleration and stopping if reduced enough, but you'd have to shed a lot more unsprung weight in other areas too before you'd really notice. Since two-piece rotors are usually sold as part of big brake kits though they benefit from being larger than the OEM one-piece rotors and it's rotor size that is the biggest factor to consider in upgrading. It's clear that you are willing to spend a pretty penny on your brake solution so you're best bet is to probably do a big brake kit for larger calipers and rotors; however, there are some finer points to brake upgrades you must consider before buying just any BBK (and I'm not talking about making sure it fits in your wheels, there's more to it than that).
If you're opting for a BBK only do one in the front and, unless you have an R or a TTRS, keep it to 4pot calipers or else you will need to upgrade your master brake cylinder too. Unless you have an R or TTRS (which are the only models I can think of off the top of my head which have more capable master brake cylinders) then anything beyond a 4pot caliper, or even a 4pot caliper with large enough pistons, will be too much for the stock master brake cylinder to properly operate. If you have a GTI or GLI or more common model like that and want to stay within the confines of what the stock master brake cylinder can reliably handle then you'll need to look at 4pot calipers such as the Porsche Boxster 986 calipers, commonly modified and rebranded by companies such as StopTech for various big brake kits on the market, and made compatible in various kits for just about every VW model. I have a ST40 BBK for my B6 (basically the 986 calipers mentioned above but with modifications made by ST) and it performs very well and does not max out the master cylinders capabilities. I'm aware of other 4pot BBK options, however, I can only speak to the quality and proper brake bias/balance of the ST40 BBK (it's very good). I can't speak to those qualities of any other BBKs out there. Look at various 4pot options and consider the ST40 BBK strongly unless you find another route that is significantly cheaper. The reason I would personally pay more for the ST40 kit than other options is because it has well done brake bias/balance which is a very important, and very often overlooked, part of a proper brake setup and braking characteristics of your vehicle. In extreme cases if someone just does willy-nilly brake mods to their vehicle and throws the brake bias far off then brake performance (as in stopping distance) can be hindered more than helped. Heat management/resistance to fade would would still be higher but otherwise a really poor brake bias can actually throw off how your car physically responds under braking. The take-away point from this is that, brake mods aren't as cut-and-dry simple as they may seem; bigger isn't always better in every way, technically there's more to it and so you want to carefully research your options not just buy the cheapest, biggest calipers you can fit.
Aside from the advantages of the above stuff, if chosen correctly, BBKs generally include stainless steel brake lines. Even if you don't get a BBK, stainless steel lines would be a good upgrade for both front and rear like the guy above me said. They will greatly improve brake feel. Also like he said, a higher end brake fluid couldn't hurt but the only reason to go crazy on brake fluid is if you're going to be seriously tracking the car. A lot of people blow tons of money on high-end brake fluids like Motul RBF, etc. but it's a complete waste of money unless your car is basically a track dedicated car; otherwise, good old ATE Typ200 (formerly often called "Super Blue") is plenty sufficient and very affordable.
The above was, of course, primarily focused at your front brake upgrade considerations. As for the rear, aside from upgrading the brake lines, you'll likely be best off with stock size rotors/calipers and just upgrade the pads. See below.
http://stoptech.com/technical-support/technical-white-papers/rear-brake-upgrades
