I bought my Brompton in 2011 (back when there was only a 5 week wait for BTO). My short test ride convinced me that the stock three speed set up 50/13 was fine, and I decided I didn't need a rack, so I got an M3L with the Shimano dynamo.
I pretty quickly discovered that I'd made a mistake with the gearing: it turns out that the low gear was about what I liked as a cruising gear; 2d gear was good for downhills, and I never really used third gear. I think this gear set up was 48-64-85.
I also decided I wanted a rack, for stability when standing as well as for "overflow" when shopping.
So the first thing I did was buy the rack kit and add it. This was more expensive than it would have been to order the rack with the bike because you also have to order a different fender. Also, it just is.
The next thing I did was to replace the halogen bulb that came with the Shimano hub with a lumotec LED light (the one that comes with the Schmidt dynamo). Unlike my other upgrades, this resulted in a significant savings: the shimano hub and dynamo cost around $110; the new LED light cost around $100-$120 (I'm not sure); but the Schmidt hub/light combination was about $500. I would recommend this approach to anyone.
But I'm still left with the high gears. So the first thing I do is buy the 44T crank and and install it. This wasn't too expensive - maybe $60? This made a significant difference, taking me down to 42-56-75, but still not quite where I wanted to be. So I switched the 13T rear cog for a 14T cog and I was at 37-49-65. This put me roughly where I wanted to be, in the sense that the mid gear was a good cruising gear, the first gear was appropriate for hills, and I did use the third gear occasionally. But I still wanted a lower gear.
So I bit the bullet and had my shop order the parts to upgrade to a six speed. This was pretty expensive - around $500, I think, primarily because you have to order a new wheel with the BWR IGH, rather than with the BSR hub that comes with the 3 speed. It also took something like 8 months for the parts to come in! Presumably because they were using them for the new bikes that were backlogged - there may have been a bottleneck with the IGH, but I'm not really sure what the issue was.
Anyway, it finally showed up about 3 weeks ago and the shop installed it for me (they did it free because of the wait, which was nice), and, at least for now, the bike is perfect. Gearing is 29-36-46-56-72-88, which gives me an extremely useful 29" gear, the 36" gear that I'm pretty used to, and two useful cruising gears - 46 and 56, as opposed to the one useful 49" I had before. 72" is useful going down hills, but I haven't used the 88" much.
It took me a couple of minutes of thought to figure out how to navigate the shifters, but it turns out it's extremely intuitive.
So apparently my job is to serve as a warning to others, at least in this context. Here is the warning (it has several parts):
1a. Do not buy the 3 spd Brompton unless you are ABSOLUTELY certain that you won't want different gearing.
2a. You won't be absolutely certain that you won't want different gearing unless you are buying your second Bromtpon.
2. You should *probably* just buy the 6 spd, but if you think you won't need all of those gears, buy the 2 speed (or single speed). That way, when you upgrade, you won't have bought *two* IGHs for one bike. (Also, the weight savings between a two speed and a 6 spd are significant; between the 3 speed and 6 speed they are not.
3. For God's sake, get the reduced gearing option unless you are going to be racing the bike or live in a town which only has hills that run downhill! (It's not a big deal or very expensive to switch if you have the right tools, however, but it's better to start low and go high than vice-versa because you are more likely to want low).
4. I think it's okay to wait on the rear rack - there's not that much of a premium to install the new one, nor is it that complicated.
5. The budget choice is to get the shimano dynamo and add the lumotec LED headlight (at least until the Shimano choice comes with an LED option.) But the SON hub is nice (and very shiny), so if you're not that price sensitive, you might want to go for that.
The cool thing about Bromptons, of course, is that you can upgrade, even years later. I kind of knew that when I bought mine, although I didn't quite realize I'd have to get a new hub to upgrade to 6. But it's still pretty awesome!
(The new wheel that I got is the new 2013 wheel with the double wall rim, so there is that).