Depending of the organism that you are looking for. Generally the database with more reliable curation are associated with single organism-like databases, for example SGD (http://www.yeastgenome.org/) for Sacharomyces, FlyBase (http://flybase.org/) for drosophila, Wormbase (http://www.wormbase.org/) for C.elegans or TAIR (http://www.arabidopsis.org/) for Arabidopsis and Genome Reference Consortium at NCBI (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/) for human, mouse and zebrafish. Beyond these databases with intensive manual data curation, other good resource for genomic database is EMBLGenomes (http://www.ensemblgenomes.org/) but the quality of the genome depends of the consortium that produced the data. Also it is interesting databases such as SGN (plants, Solanaceae) where you can find a community curation model based in the assignment of Locus editor role to relevant publication authors (http://solgenomics.net/).

About the software to build metabolic networks, I like Pathway Tools (http://bioinformatics.ai.sri.com/ptools/) associated with MetaCyc database, but there are other options such Blast2GO for annotation (http://www.blast2go.com/b2ghome) and KEGG pathways (http://www.genome.jp/kegg/pathway.html) or Mercator (http://mapman.gabipd.org/web/guest/mercator) for annotation and MapMan (http://mapman.gabipd.org/web/guest/mapman).

Depending of the organism that you are looking for. Generally the database with more reliable curation are associated with single organism-like databases, for example SGD (http://www.yeastgenome.org/) for Sacharomyces, FlyBase (http://flybase.org/) for drosophila, Wormbase (http://www.wormbase.org/) for C.elegans or TAIR (http://www.arabidopsis.org/) for Arabidopsis and Genome Reference Consortium at NCBI (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/) for human, mouse and zebrafish. Beyond these databases with intensive manual data curation, other good resource for genomic database is EMBLGenomes (http://www.ensemblgenomes.org/) but the quality of the genome depends of the consortium that produced the data. Also it is interesting databases such as SGN (plants, Solanaceae) where you can find a community curation model based in the assignment of Locus editor role to relevant publication authors (http://solgenomics.net/).

About the software to build metabolic networks, I like Pathway Tools (http://bioinformatics.ai.sri.com/ptools/) associated with MetaCyc database, but there are other options such Blast2GO for annotation (http://www.blast2go.com/b2ghome) and KEGG pathways (http://www.genome.jp/kegg/pathway.html) or Mercator (http://mapman.gabipd.org/web/guest/mercator) for annotation and MapMan (http://mapman.gabipd.org/web/guest/mapman).

I would also check out the NAR database site, http://www.oxfordjournals.org/nar/database/c/ there is an extensive list of specialty databases.

I like Ensembl most - the completeness of data is at least comparable to NCBI-ones, but it is much better organized in terms of structure and access modes, things like bulk downloads of the database, biomaRt, homologs finding... For the species not present in Ensembl, you need to use a specialized one, as Aureliano writes.

I would also go for Ensembl. Nonetheless, if you have a specific requiremente you should go for the specific database, as it will tend to be most up to date.