A methodical way for designing perfboard layouts

Howard Johnson has a massive collection of high-speed digital design newsletters.

http://www.sigcon.com/pubsAlpha.htm

One of my favorites visibly demonstrates the return currents that darron mentioned. DC will flow in a straight line (the path of least resistance; a straight line on the ground plane), while AC will flow underneath the signal conductor (the path of least inductance; a mirror image of the signal path on the ground plane) So avoid having that return path cross a split plane, avoid having it cross too many other high-speed return paths, etc. Also, power planes can act like ground planes for a return path, and the return path can jump planes through a capacitor (remember, cap is a short to high frequencies); the return path always chooses the plane closest to the signal. http://www.sigcon.com/Pubs/news/8_08.htm

I believe there are other newsletters. For instance, 90 degree angles aren't really that bad; they merely add excess capacitance to the trace. At "regular" high speed frequencies, this is no big deal. But when you hit microwave, the parasitic capacitance can do you in. http://www.sigcon.com/Pubs/edn/bigbadbend.htm

Regarding trace size, this largely depends on your stackup. If you use a solid reference plane (ground or power!), then your trace impedance is a function of trace width and distance from the plane. If you don't care about the impedance, then trace size largely doesn't matter, as long as it's not too small. Unless you're trying to carry obscene amounts of current (amps?), in which case you need traces big enough that they won't melt!

Try to keep signal planes adjacent to reference planes. i.e. for an 6 layer board, signal layers 1 and 3 reference ground plane 2, and signal layers 4 and 6 reference power plane 4. If signal planes are adjacent, be careful that there are no long parallel runs that could induce cross-talk. This is less of a concern if there's a reference plane (although the return currents can still cross-talk, it's not as bad)

Keep clock traces and other strong sources of noise as far away from other traces as you can (I think the rule of thumb is 5x the trace width away for clocks and 3x for other switching signals).

Yes.

For simple circuits, so long as all the same electrical connections exist then the circuit is equivalent.

(Only for high speed or some analogue circuits do wire length and shape start to have effects)