I found transmission to be quite nice. It stores its configuration in JSON, has a console interface, can run as a daemon with a web interface and it has GTK/Qt guis (though those are quite sucky indeed). It also supports magnet links and PEX.
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GCS/IT/M d- s+:- a-- C++ UL+++ US UB++ P+++ L+++ E--- W+ N+ o--
K- w--- ?O M-- ?V PS++ PE- Y++ PGP+++ t+ 5 X+ R tv b+++ DI+++
D+++ G+ e h! r y+
Gregor Best
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