Thanks for the cool tools Maria! These will definitely help me out. Hopefully we'll get some more great answers like yours! I've listed some of my favourites below:

Exploring your Data in the context of Encode:

http://epiexplorer.mpi-inf.mpg.de/

Epigenetics and Promoter Sequence Tools:

http://mpromdb.wistar.upenn.edu/

http://meme.nbcr.net/meme/

http://insulatordb.uthsc.edu/

Genomically Imprinted Genes:

http://www.geneimprint.org/site/genes-by-species

http://www.mousebook.org/catalog.php?catalog=imprinting

Venn Diagram Creators:

http://bioinfogp.cnb.csic.es/tools/venny/

http://www.cmbi.ru.nl/cdd/biovenn/

Protocols:

http://openwetware.org/wiki/Main_Page

Hi, may be not "lesser known" but for me almost in everyday use:

EnrichR (http://amp.pharm.mssm.edu/Enrichr/)

iHOP (http://www.ihop-net.org/UniPub/iHOP/)

ArrayMining (www.arraymining.net)

BioModels.net

Bio-web (http://www.cellbiol.com/)

Thanks for the cool tools Maria! These will definitely help me out. Hopefully we'll get some more great answers like yours! I've listed some of my favourites below:

Exploring your Data in the context of Encode:

http://epiexplorer.mpi-inf.mpg.de/

Epigenetics and Promoter Sequence Tools:

http://mpromdb.wistar.upenn.edu/

http://meme.nbcr.net/meme/

http://insulatordb.uthsc.edu/

Genomically Imprinted Genes:

http://www.geneimprint.org/site/genes-by-species

http://www.mousebook.org/catalog.php?catalog=imprinting

Venn Diagram Creators:

http://bioinfogp.cnb.csic.es/tools/venny/

http://www.cmbi.ru.nl/cdd/biovenn/

Protocols:

http://openwetware.org/wiki/Main_Page

Nice topic,

Not bioinformatics but still amazingly useful:

http://www.chemicalize.org/

The "sequence manipulation suite" at Bioinformatics.org: http://www.bioinformatics.org/sms2/

GeneDoc- version for Mac should be coming out early next year. http://www.nrbsc.org/gfx/genedoc/

not sure that these are 'lesser known' but i use them all the time

GETprime - qPCR primer design http://updepla1srv1.epfl.ch/getprime/

Metacyc - metabolic pathways http://metacyc.org/

KEGG - metabolic pathways http://www.genome.jp/kegg/

Oligo Analyzer - primer design http://www.idtdna.com/analyzer/applications/oligoanalyzer/

DAVID - GO enrichment tool http://david.abcc.ncifcrf.gov/

C. elegans specific tools:

Wormbase Wormmine - database query tool http://www.wormbase.org/tools/wormmine/begin.do

SPELL for finding which genes are co-expressed with your favorite genes in other people's data: http://spell.caltech.edu:3000/

Wormnet - find genes that functionally cluster with your favorite genes http://www.functionalnet.org/wormnet/cgi-perl/WormNet.v2_nga_form.cgi

I would like to mention about TRANSPATH - a database about signalling molecules and signalling pathways

http://genexplain.com/transpath-1

and GeneWays - protein-protein interaction database

http://genexplain.com/geneways

Recently published comprechensive classifiaction of transcription factors

http://www.edgar-wingender.de/huTF_classification.html

"TFClass: An expandable hierarchical classification of human transcription factors". Nucleic Acids Res. 41, D165-D170 (2013). doi: 10.1093/nar/gks1123 (http://nar.oxfordjournals.org/content/41/D1/D165.long)