I have mentioned the importance of front-end frame geometry, but the rear of the bike is equally critical if a comfortable ride is to be had over a long distance. Key factors are seat tube (ST) angle and chain stay (CS) length.
Seat tube angle
The ST angle affects position fore and aft on the bike. A ST angle of 73 degrees is a typical compromise, however, some account must be taken of the purpose of the bike. When riding long distances top-heavy riders might require a shallower angle to bring their weight back off the handlebars, whereas bottom-heavy riders might require a slightly steeper angle for the opposite reason. Racing bikes, where comfort over long distances is less of a premium, will generally have a steeper angle which results in a more forward position for power sprinting. However, everything is a compromise, so the ideal ST angle will depend on rider physiology and the main type of riding that will be encountered.
Longer chain stays give a 'springier' ride and give more clearance between the ST and wheel, allowing mudguards to be fitted, so this geometry is advantageous on touring bikes. Racing bikes have short chainsays because mudguards are not required and the more compact geometry improves handling and maximises power transmission to the rear wheel.
If you want to fit mudguards then there must be enough clearance between the rear wheel and the ST and the front wheel and fork crown, so the CS length and fork length must be adjusted accordingly, at the same time taking account of wheel and tyre size.
700c wheels have become the de facto standard on most road bikes, and 26" on mountain bikes. There is no particular reason for this other than historical accident and other sizes have been used on bikes in the past: 650b was used on French randonneuring bikes; and 650a on english 3-speeds. The aforementioned wheel sizes are actually diameters of the wheel with a particular tyre fitted. Standard sizes follow the ISO (formerly ETRTO) system which designates the wheel rim diameter as measured between the the bead seat, so a 700c wheel is actually ISO 622 with a 39 mm wide tyre (622 + 2 x 39 = 700). So, the actual sizes are:
700c = ISO 622 with 39 mm tyre designated 39-622
26" = ISO 559 with 50 mm tyre designated 50-559
650b = ISO 597 mm with 26 mm tyre designated 26-597
For a comprehensive treatment of this topic I recommend the late Sheldon Brown (Brown, 2013).
Brown, S. (2013). Tyre Sizing Systems. Available at http://sheldonbrown.com/tire-sizing.html [Accessed 22/092013].