Useful bookmarks for probe and primer design:
 
http://www.operon.com/oligos/toolkit.php
 Use free online Tm calculators to see what the Tm for primer and probe sequences are. We use the Operon calculator, as it also has a good tool to check possible primer-dimerization sequences. Reach it from www.operon.com then select DNA Synthesis, then select Oligo Toolkit.
http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi
 This is a link to Primer3 software. It is software that allows for primer design and also helps picking an internal oligo sequence to these primers (a probe sequence). Like most primer design algorithms, it has the disadvantage of not taking into account secondary structure issues that are paramount in primer/probe design for real-time PCR. With that caveat in mind, it is a good place to start the design process, if you are not inclined to do it by eye (i.e. scanning the sequence yourself). Then you can check your sequences at the folding site (described below).
http://www.ncbi.nlm.nih.gov/BLAST/
 This is the site for the Basic Local Alignment Search Tool from the National Center for Biotechnology Information. Use this site for checking specificity of probe and primer sequences.