Once I decided that I wanted to build a small table-top sized railroad, I had to come up with a track plan.  I didn't even know whether I wanted to model HO or N scale.  I had modeled N scale back in the mid-80s, but the quality of the models were not where I liked it, and that meant that the engines and cars didn't give me the sense of mass that the prototype does.  Instead, the commercial equipment gave me a sense of "mini-Lionel" with the oversized wheels, track, and other items.  So, I initially planned on doing a 4'x6' switching layout in HO scale.  I started by researching track plans online, in magazines and books, and sketching out some plans of my own. 

While looking through Kalmbach's 101 Track Plans, I came across the award winning plan #15, which was 4'-6" x 5' in HO.  The designer (W.R. Budd) included a few spurs, no runaround track, yet he managed to include three loops in the mainline.  This amount of running in a small area intrigued me, and I considered using this three loop arrangement for a simple little N scale layout in addition to the HO switching plan.  As I was sketching out different possibilities, I wondered how adding a passing siding and spurs would work out.  The more I tried different designs, the more I liked the idea of doing my main layout in N scale with the triple-loop arrangement.  Soon, I had a basic triple-loop arrangement with a passing siding that would fit into a 2'-6" x 5' layout, which could be put into a coffee table somewhere down the line if I wanted to.

But I had to address the drawbacks of N scale before I continued.  One was that code 80 rail looks very awkward to me, and I wanted as small of a rail size as possible.  The only commercially available code 40 turnouts were expensive kits that needed to be special ordered, and required enough work that one might as well handlay them.  I didn't feel that I was up to that yet, so I passed on them, and looked to code 55.  For commercially available no. 4 turnouts, Peco was about the only option.  Personally, the rail height is more important to me than correct tie spacing, so that's what I went with.  Since then, Atlas has come out with some code 55 track, but their smallest turnout (no. 5) still would have been a significant compromise, so I don't think I would have gone with them even if they were available when I was starting this project.  Micro-engineering does offer code 40 flextrack, so I purchased some for use in most spurs.  When laying them, I simply cut and spread out the ties to match the Peco track, and they blend together pretty well.

After that had been figured out to my satisfaction, I looked at the quality of contemporary engines and rolling stock, and the availability of things like engine detail parts.  I found plenty of detail parts, decent rolling stock, and low-profile wheels from Micro-Trains, which was enough to meet my needs.  I would be able to put the "mini-Lionel" feel of the older N-scale equipment in the past, and get the sense of mass that I was looking for.  So the decision was made, I would stay in N scale, and build a small layout based on the triple-loop design.
 
This is the initial track plan that I came up with:
Once I got the plan to a basic point that included what I wanted, I moved on to a full size mockup to determine final details and arrangement.  I spliced together two pieces of 3/8" foamcore cardboard to make a 2'-6" x 5' sheet for the mockup.  I purchased some Peco turnouts and used other track pieces that I already had to draw an accurate plan on the foamcore.  There are 3-D computer packages available so that one could do this on the computer, and get a sense of how big you'd want a mountain, how steep of a hill, and things like that.  But with a small layout such as this, I can get a good idea of what I wanted without having to spend money on and spend time to learn another program.  I wanted to get building!  Now if I design a multilevel room layout, the time and money spent on a program would be worth it.

I was able to verify that the track spacing would work for me with the mockup, but I made a few other modifications.  Having the town area and the inside loop butt up against a steep hill where a tunnel is for the middle loop on the right end would have been very awkward, so I flipped the inside spur to point the other way, and put the inside loop under a tunnel on the right end.  That tunnel ended up separating the inside loop into two different scenes, hid the 9 3/4" radius curve, and made that end of the layout look less like a slot-car track.  I also turned one of the inside loop tracks into a gentle S-curve to offer a little variety.

At this point, I noticed that there was room under the passing siding for a couple of tracks that I could use as staging, so I put as much track under there as I could.

The tracks highlighted in red in the illustration below show the changes which were made.
At this point, I got my Homasote and other lumber, drew the track plan and cutout markings on the Homasote, and did another mockup with this revised plan to make sure that everything worked well together.  I chose Homasote because I was familiar with it compared to foam.  More importantly, with all of the close cuts, small pieces, and narrow subroadbed required, I didn't think that foam would be strong enough in some areas.

Below is a shot of the mockup process when I was in the middle of drawing the final track plan on the Homasote.  The track is marked in black, while cut locations are marked in red (although it is hard to tell the color difference in some portions of this picture).  You can see how I used empty car boxes, tunnel portals, and things like that to put the track at different elevations to better imagine the final layout in 3D.
My mistake was that I didn't slow down and mock up the final design after I made my changes.  After the Homasote was cut out, the frame built, and all of the track laid and wired up, I noticed that there was a big area inside the loop on the right end which had nothing in it.  There was enough space for a spur and mine with little changes needed at that point, and it would also allow me to add a small wood trestle.  You can see in the picture above that the mine inside the loop is missing.  Fortunately, the homasote was at the right elevation for the mine, so all I had to do was cut out a stretch of track, cut out a hole for the switch machine, and cut out another hole for the uncoupling magnet.  The picture below shows the area with everything cut away, ready for new roadbed and track to be added.  Once that was installed, I was finally done with track planning.