I am really satisfied with CQRLog for Linux. It support CW keying, general logging, DX cluster, eQSL, LOTW, hamQTH and QRZ.com search. It was developed by OK1CQR and OK1RR. It uses mysql as database server, cwdaemon for cw keying.
CQRLog also support for digital operation, transceiver control and WinkeyUSB keyer. But, it lack of support for contest templates, rotator control and also cw repeat message. Hopefully that the developers will add this support.
For more info, please visit http://cqrlog.com/