Here are some quick entry points to help orient you towards common tasks:
Find documentation about all the methods available to a particular object
You should see the Deobfuscator to find out this info. Unfortunately, some modules are better documented than others - we are trying to work on this.
Process a sequence file to get the sequence or to find the exon locations
Count the number of hits for each query from a BLAST report
Process a Clustalw formatted alignment
Use Bio::AlignIO to parse multiple sequence alignments. If one wanted to convert the alignment into a NEXUS multiple alignment format for running with PAUP and MrBayes, use Bio::AlignIO::nexus. If one wanted to run a PHYLIP program use the Bio::AlignIO::phylip module to convert the alignment into PHYLIP multiple alignment format.
Read a phylogenetic tree file
Parse MEME output and manipulate motif information
Check to see if a certain script has already been written
Go to the Bioperl scripts page.
Parse the output from Gene prediction programs
Run population genetics tests
The PopGen HOWTO provides an introduction to the PopGen modules. Statistics are calculated with Bio::PopGen::Statistics while the Bio::PopGen::Utilities provides functions for converting alignments to Bio::PopGen::Populations.