Agreed with DocF - Spocalc is very nice. I also like the one that is on the http://www.bikeschool.com/ site. Just use the link in the left hand column when you get there. I think it's a good idea to use two different systems as a cross check until you've done a few. One thing you need to be REALLY careful of is how you measure E.R.D.(effective rim diameter). Depending on who you believe, it get's measured differently. Spocalc says measure the nipple length as dimension "B" and say it's the length of the nipple. Barnett's says "Measure and record nipple length (NL) from the bottom of the slot to the tip of the nipple". This means the bottom of the screwdriver slot in the nipple. Since the screwdriver slot is ~2mm and you have two nipples in the E.R.D. measurement, whether you use the slot, or not, will change the E.R.D. dimension by up to 4mm (!!!). Measure everything as accurately as you can. I measure to tenths of millimeters. If you are doing the E.R.D. with a "naked" rim, do several measurements and average them out. Why all the fuss?
If you use good quality spokes, you are going to be close to $50 in spokes for the two wheels. Speaking of which, straight gauge spokes are about $9/pkg of 20 from Nashbar and you will need four pkgs to lace both wheels. For about $3 more per package you can get the nice 14/15/14 double butted spokes which any wheelbuilder worth his salt will tell you are superior to straight gauge - for many reasons. If you are going to put forth the effort to build nice wheels, isn't it worth it to spend another $12 and get great spokes? I suggest the DT Competition 14/15/14(or 2.0/1.8/2.0mm). If you do a really good job building, these spokes will give superior performance and should never break. So, do your measurements as accurately as you can, use two different systems to cross check, and use good quality spokes. Taking the time to get it right is much easier than to have to unlace the wheel and know that you have wasted a fair amount of money on the wrong spokes.
Also, check out "Sheldon Brown's Excellent Wheelbuilding Page" which is linked from the bottom of the Spocalc page. For totally anal wheelbuilding, including exhaustive tension balancing, I'd say Barnett's Manual is most complete.
So, take your time and do a good job. And then enjoy your new wheels ;-)