Comprehensive list of microRNA target database and softwares as follows:
(1)miRBase: it is a gold-standard database of microRNA sequences. it provided links of microRNA targets predicted by other target predictions, such as PicTar. release date: Sept, 2010. website: http://mirbase.org/
(2)starBase: A public platform for exploring miRNA-target interactions from CLIP-Seq (HITS-CLIP, PAR-CLIP) and degradome sequencing (PARE) data. It also provides intersections of multiple target predictions, such as Targetscan, PicTar, miRanda, PITA, RNA22 and miRSVR. release date: May, 2011. website: http://starbase.sysu.edu.cn/
(3)TarBase: A database of experimentally supported animal microRNA targets. release date: January, 2009. website: http://microrna.gr/tarbase/
(4)miRecords: an integrated microRNA target database. It provides miRNA-target relationships predicted by multiple target predictions, such as Targetscan, PicTar, miRanda, PITA and RNA22.
(5) targetScan: a well-known software for predicting microRNA targets from conserved UTR sequences. It was developed by Bartel lab. release date: April, 2009 (v5.1). website: http://www.targetscan.org/
(6) PicTar: a software for predicting microRNA targets by combining multiple microRNAs or targets. It was developed by Rajewsky lab. release date: March, 2007. website: http://pictar.mdc-berlin.de/
(7) PITA: it predicted microRNA targets based on target-site accessibility and minimum free energy. release date: August, 2008. http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html
(8) RNA22: it is one of popular microRNA target prediction softwares. release date: 2007. website: http://cbcsrv.watson.ibm.com/rna22.html
(9) miRanda and microRNA.org. It include software(miRanda) and database (microRNA.org). The newest version of miRanda also be called mirSVR. release date: August, 2010. website: http://www.microrna.org/microrna/home.do
(10) MicroCosm: it is a microrna target database developed by Enright lab at EMBL-EBI. release date: August, 2010. website: http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/
(11) miRTarBase: a experimentally verified miRNA target base. October, 2010. website: http://mirtarbase.mbc.nctu.edu.tw/index.html
（12）miRGator v2.0：a integrated database of microRNA expression and targets. release date: November, 2010. website: http://mirgator.kobic.re.kr:8080/MEXWebApp/
（13）MiRNAMap: a integrated database of microRNA and their targets. January, 2008. website: http://mirnamap.mbc.nctu.edu.tw/
(14) miRDB: animal microRNA target prediction and functional annotation. release date: August, 2010. website: http://mirdb.org/miRDB/
(15) RNAhybrida easy, fast and flexible software for predicting microRNA targets. release version: v2.1. website：http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/
For Plant microRNA targets:
(1) Targetfinder, predicts small RNA targets in a sequence database using a plant-based scoring metric. release date: Aug, 2010. website: http://jcclab.science.oregonstate.edu/node/view/56334
(2) starBase: A public platform for exploring miRNA-target interactions from degradome sequencing (Degradome-Seq, PARE) data. release date: May, 2011. website: http://starbase.sysu.edu.cn/
(3)miRU, psRNATarget: an automated plant miRNA target prediction server. website: http://www.plantgrn.org/psRNATarget/
(4) CleaveLand, a pipeline for using degradome data to find cleaved small RNA targets. release date: March, 2010, website: https://homes.bio.psu.edu/people/faculty/Axtell/AxtellLab/Software.html
(5) Target-align: a tool for plant microRNA target identification. release date: 2010, website: http://www.leonxie.com/targetAlign.php
new miRNA target database.
(1) ChIPBase, decoding the post-transcriptional and transcriptional regulation of microRNAs from CLIP-Seq and ChIP-Seq data. It constructed TF(transcription factor)->microRNA->targetsregulatory networks.
(2) doRiNA: a database of RNA interactions in post-transcriptional regulation.
Thanks for the useful links. Do you know about the Nucleic Acids Research Online Database (see links on right hand side of page here)?