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If you found a gene in EnsEMBL or Vega and want its sequence, you can simply use the download options 'export cDNA' or 'export peptide' that appear with a mouse over. To generally download data from EnsEMBL, you can use the ExportView pages at http://www.ensembl.org/Danio_rerio/exportview where you will be offered the option to export features and sequence in a range of different formats.
For Vega, this is possible at http://vega.sanger.ac.uk/Danio_rerio/exportview.
To download pre-generated EnsEMBL datasets, try http://www.ensembl.org:80/Download/.
For more advanced types of data retrieval from EnsEMBL, the EnsMART tool is extremely useful (http://www.ensembl.org/Multi/martview as described below)