(1) ChIPBase: ChIPBase is a database for annotating and exploring the expression profiles and the transcriptional regulation of lncRNAs and other ncRNAs.
http://deepbase.sysu.edu.cn/chipbase/

(2) lncRNABase: for decoding miRNA-lncRNA(lncRNAs, circRNAs, pseudogenes) and miRNA-ceRNA interaction networks from CLIP-Seq datasets.
http://starbase.sysu.edu.cn/mirLncRNA.php

(3) lncRNAdb: contains a comprehensive list of lncRNAs that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. website: http://www.lncrnadb.org/

(4) LncRNADisease: a database for long-non-coding RNA-associated diseases.
http://cmbi.bjmu.edu.cn/lncrnadisease

(5) LNCipedia: a database for annotated human lncRNA transcript sequences and structures.
http://www.lncipedia.org

(6) NONCODE: NONCODE provides an integrative annotation of long noncoding RNAs.
http://www.noncode.org

(7) NRED (ncRNA Expression Database):  provides gene expression information for thousands of long ncRNAs in human and mouse. It also contains both microarray and in situ hybridization data, much of which is described here for the first time.
http://jsm-research.imb.uq.edu.au/nred/

(8) PLncDB: Plant Long noncoding RNA Database.
http://chualab.rockefeller.edu/gbrowse2/homepage.html
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From:
http://www.protocol-online.org/forums/topic/31018-comprehensive-list-of-long-noncoding-rnalncrna-resources/