Another thing to consider are your local building fire codes. This means you will need to use Plenum cable in any fire-rated space (typically in drop ceiling areas, stairwell walls, etc.).
Tips for a good wiring job for a hobbyist or DIY'er:
1. Well terminated ends are the most important thing, as that has the largest impact on your end result.
1a. If it's punch down blocks, then all of the wires need to be well seated and not under tension.
1b.If you're talking RJ11/45 plug ends, they need to be well seated and crimped securely. If you have a problem with the plug-ends, use the EZ-Crimp kind where the wires can go through the end of the plug. This requires a special crimping tool with a razor that trims the end flush, but it can make it a bit quicker and easier.
1c. Remember that each wire is likely to be moved back and forth at the punch panels. Give a bit of slack for future techs to work with. Remember things like extra wire at the patch panel if it is on a swing arm, a few coils of extra wire at drops in the ceiling space will allow flexibility on later work, and cutting a foot longer than you need gives you "crimping/punch-down screw up room".
2. Network Cable boots help the tension problem and are a nice, easy way of making professional looking patch cables. You can also use those to color code connections.
3. Pay attention to Sheathing. The basic concept is using a small run of pipe to make a nice transition between locations. This could be between rooms through a wall, or from a drop-ceiling space down into your wiring closet. There are straps that will secure the sheath to the wall above the ceiling line. This is also a requirement in some fire codes between certain spaces, so again - be sure to check the code requirements for your particular state, city & county.
4. Zip ties are your friend. Nothing looks better than trimmed zip ties bundling your runs together, especially when you get to the patch panel. It is VERY important to remember why a cat 5e or cat 6 is rated that way; it's how tightly the copper is twisted together. The tighter the twist results in cleaner signals, which in turn equals category. Bends, crimps and pinches are to be avoided at all possible cost. Gentle curves are king and tight zip ties are the work of the devil.
5. Spend the money on good tools. Cheap (read: Crappy) Crimping, punch down and stripping tools not only damage your work but they slow you down. It's already not a fun job - it's a horrible job when you're trying to do it on the cheap.
6. A cable signal tester is a must! Nothing is worse that doing all the work, plugging it in and realizing that you are too close to a power line and the interference has ruined a 20 cable run that limits your 1000Kbs connection to 10kbs.
7. Remember to label your wires end to end. Confusion will make the job slower.
8. Short range walkie talkies are handy when you're trying to coordinate with another person to pull, stop or start feeding your cable three floors away. Specifically ones with hands-free headsets.
9. If you're replacing existing wall jacks: Consider making every drop at least a quad-box. Many more things are using network outlets, especially printers and phones (which is the point of what you're doing). Having only 1 or 2 outlets per panel is short-sighted and a bigger pain to add to later on.
10. If you're adding new wall jacks: Remember that you want any outlets within 5' of a power outlet in general. Standard height for any outlet box (telco/network/electric) is 1'6" from finished floor to center of box. Older installations will probably be lower. #9 still applies.
11. Document and label all plugs/punch down locations! A map layout is preferred, but the least you should do is match the number at the patch panel to the wall plates.
