Synthetic Biology is an interesting site about the branch of science informally described as "[m]aking life better, one part at a time" or more formally:
A) the design and construction of new biological parts, devices, and systems, and
B) the re-design of existing, natural biological systems for useful purposes.
Whether one believes that reverse engineering and re-designing organisms is a worthwhile goal, it is certainly the holy grail for a biohacker. The site looks like an excellent resource for someone deciding whether they want to join the field.
The Online Artificial Gene Design discussion on Slashdot produced several suggestions for software that can help in design and analysis of DNA sequences, in addition to the Gene Design suite that started the discussion. Unfortunately, only one of the suggested resources – Sequence Manipulation Suite – has a significant number of DNA analysis tools that may be useful for oligonucleotides.
A collection of tools for designing and manipulating DNA sequences is offered on the Gene Design website at Johns Hopkins School of Medicine. The authors are not clearly identified on the website, but New Scientist reported that:
GeneDesign was created by researchers led by Jef Boeke at Johns Hopkins University School of Medicine in Baltimore, US.
This set of tools for designing and analyzing DNA sequences and for selecting restriction enzymes and vectors has a few features I find appealing in software: university-developed, web-based, free, and open-source. Several similar resources were suggested on Slashdot.