I've been out for a while, but here are other songs that aren't on that list and some info about some songs.
As far as Sister goes, it has been officially released twice by the band. There is a hidden version on Love Your Ground, which follows The Banjolin Song. There are also 2 versions of Feel The Tide, and 2 versions of The Banjolin Song.
And covers, there's a cover of I'll Fly Away (folk song), Tell It To Me (with OCMS), Lady of the River (with Cadillac Sky, King Charles), Unfinished Business (White Lies Cover), Come Thou Fount of Every Blessing (Traditional).
There are 2 official versions of Hold On To What You Believe, an official version of To Darkness, an official version of Nothing Is Written (but when it was recorded under the name Untitled), 2 official versions of The Cave, 2 official versions of Winter Winds (one under the name But My Heart Told My Head), 2 official versions of Little Lion Man (much like The Cave and Winter Winds, it has been released officially about 3 times, but only 2 different versions).
There are also 2 versions of Liar, one of which is Marcus' original song as him performing it himself, which features an additional verse.
Marcus' solo stuff has 2 versions also, there are 2 different versions of Wretched Man (the only difference is one is live and has less of the song's lyrics because he left them out), and 2 versions of Will I Praise Again (which you all call You Ain't No Sailor, but is really called Will I Praise Again). There is a live version that has less or rather different lyrics than the recorded version.
Hope that helps :)
keep smearing my heart all over my sleeve, then someone comes and wipes it off, and takes it from me.