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The question of how to choose the 'right' bike is discussed in detail on various overlanding/motorcycling discussion forums. A little bit of research sure isn't a bad thing, and forums can help to identify a bike's weakpoints.
Chris Scott's "Adventure Motorcycling Handbook" was a good starting point for looking into travel-worthy bike options. For me it all came down to personal preference, road/off-road capabilities and the planned route.
After some basic research & trying a few bikes I decided to go for BMW's F650 GS Dakar. This chain-driven single cylinder enduro/dual-sports has been around for quite a while now, with regular updates every few years. It is mechanically simple & easy to fix, very economical, doesn't lose power/torque in high altitude areas (thanks to the fuel injection) and very comfortable to ride. Compared to the standard F650 GS, the 'Dakar' version has slightly more emphasis on off-road riding, with a thinner & larger 21" front wheel, a slightly better rear shock and a higher seat.
Generally, the build quality is fairly good & most of the F650's know problems areas can be overcome whilst prepping the bike for the journey and by taking the appropriate spare parts (wheel bearings, head bearings and water pump repair kit).
Luggage
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I went for "hard luggage" aluminium panniers from Overland Solutions. Waterproof, safe against theft, easy to take off, and sturdy enough so it stays on the bike in case of an accident/off.
One downside of hard luggage: it's potentially dangerous in an accident, as the legs might get caught in the panniers.
Overland Solutions provided a really good pannier system: 3mm waterproof aluminium panniers (32l each), lockable with replaceable padlocks, and a sturdy metal frame with a 'shelf-style' system to place the panniers securely. The frame has plenty of space to attach tie-down straps and bungee-cords to hold extra fuel & water when necessary. On the inside of the frame (below the exhausts) are 2 small additional boxes to hold tools, spares and everything else I don't need on a daily basis.
The tankbag is from Touratech: expandable and with 2 soft side panniers (optional/zip-on). It was only water-repellant, so I made up a waterproof insert from an old sleeping mat. The tank-bag will hold my camera equipment for easy access.
Trip-Update: Albeit quite heavy, I've been really happy with the whole luggage system. So far, I dropped the bike twice whilst offroading and the pannier corner only has a small dent (about 2mm, so not even worth mentioning). As I found out in a deep water crossing in Australia's Kakadu National Park: everything's still waterproof.
Only nuisance: I had a few broken/sheared sub-frame bolts (the ones behind the engine). The pannier frame is supported by those bolts, and I have now upgrader them from M8 to M10 + lock-tite.
Bike Modifications
There are plenty of aftermarket modifications available from various manufacturers, yet I tried to stay away from most of them & only went for what I thought was important to me.
Sheep skin on the seat bench (hence the bike's name "Dolly")
My parents kindly 'sponsored' the sheep skin that's been lying in their bedroom for as long as I can think. Good in hot areas, not so good when it rains. But it is indeed more comfortable than just the plain black plastic cover. (A fellow overlander friend told me his bench got so hot in the Chinese Taklamakan desert, he couldn't ride in a seated position)
Handle-bar raisers and 'Throttle Rocker'
Raising the handle-bars improves comfort, especially for tall people (I'm 1.86m). Due to working with computers for a long time, I suffer from RSI / carpal tunnel syndrome in my wrists. Handle-bar raisers help me to maintain a healthy riding position, with a comfortable angle between lower arm and hand. Also, when standing in the foot-pegs (offroad), the handle-bars are easier to reach.
Trip-Update: I binned the throttle rocker and replaced it with a bit of inner tube, wrapped around the mirror and handlebar. This creates enough friction & works a treat as a DIY cruise control.
Progressive fork springs
The F650's original front suspension is quite soft, and a fully-laden bike can 'dive in' quite a lot when breaking hard (or in off-road use). I fitted progressive fork springs in conjunction with thicker suspension oil (10W) in order to increase bike handling.
Metal chain guard
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Not really necessary, but: The original chain guard was broken anyway (giving a rattling noise when hitting the swingarm).
Trip-Update: The bike's screw-mount for the chain guard broke off in Tajikistan, and I've since been riding without it without any problems. The Australian MOT in Darwin was pretty relaxed about it as well, although they mentioned I should get a replacement.
Chain Oiler
Another cheap but very good option: the Loobman chain oiler (£18 inc postage). I picked it up in London from the guy who makes them. The system feeds through gravity and works with anything from engine oil to olive oil. A good squeeze on the oil container bottle prior to setting off – sorted. At 4-5x the price "Scottoilers" might look more professional, but I heard it can be a problem to adjust the correct oil flow. Whenever possible, I try to fill up with some ATF (Automatic Transmission Fluid for cars), as it's said to be a good chain oil.
Trip-Update: The chain oiler's been very good, and ATF is readily available everywhere. Only downside of the Loobman: the cable ties (which act as leads for the lubricant) need replacing every now & then. They're standard size and I always carry some spare ones with me anyway.
Whilst cleaning the bike in East Timor (for Australian Quarantine Inspection), I threw the Loobman away. Once I've got some bucks spare, I'll upgrade to a Scott Oiler for convenience.
Aluminium front sprocket cover, rallye foot-pegs, Engine Crash Guard
The new cover (Touratech) makes it easier to clean the front sprocket, and in case of an extremely worn-out (and snapped) chain it helps to protect the engine housing.
The foot-pegs had been fitted by the previous owner. Overland Solutions added a more stable mounting (the black bit in the photograph), which also protects the brake pedal.
Additional Auxiliary Power Socket
The F650 already comes with a power socket (on the left hand side near the engine). I put an additional one near the dashboard, so I can easily run a cable into the tankbag for charging my mobile phone/camera batteries/AA batteries, or the GPS.
Battery
I replaced the original battery with an 'Odyssey PC310' or 'Hawker' dry cell battery . It provides a higher cranking power, doesn't leak in an off – and it's smaller than the original battery. This leaves some extra space underneath the battery, to carry some spares such as brake pads. Cheapest supplier I could find in the UK were "Knight Batteries".
Trip-Update: I've been running the Odyssey/Hawker battery for over a year now. Worst conditions so far were in Tajikistan, when a combination of cold temperature and bad engine oil (fake 'Shell' import from China) glued up the clutch and the engine wouldn't turn over. No problem for the battery.
Brake Cylinder Protection
The rear brake cylinder is fairly exposed, so I made up a protector from a 3mm aluminium sheet & bent it so it fits snuggly and doesn't touch the right foot's heel. The protector simply screws on top of the brake cylinder (using the original bolts).
(A friend told me afterwards that the brake cyclinder from one of the bigger BMW bikes (1150 or 1200 GS I think) is very cheap & fits perfectly).