I was hoping to gather a list of useful sites for asking bioinformatics questions. I've just come across BioStar recently, and I like the fact that almost all questions are answered. Up to now, I've been using two sites:
http://www.seqanswers.com is an excellent site for general sequencing questions and answers. It is a discussion forum rather than a Q&A, so I find that a significant number of questions go completely unanswered. They've recently added a Q&A component (http://i.seqanswers.com), but it doesn't appear to be catching on.
http://groups.google.com/group/spctools-discuss is a mailing list for discussing the Seattle Proteome Center's tools (e.g. TPP), but can be used for general proteomics queries.
Some answers summarised:
http://stats.stackexchange.com is a Q&A for statistical analysis (thanks Pierre)
The BioConductor mailing list is a good place to go with R BioConductor questions, and also for general help with statistics/experimental design (thanks Daniel Swan)
http://stackoverflow.com can be used for general programming questions which come up in bioinformatics. Ofter a very fast turnaround (thanks Daniel Standage)