In earnest:
1) Warm up my body. I normally grab my bokken (wooden kendo sword) and do 20 or 30 swings to get my arm muscles and heart warmed up
2) scales/arpeggios. Normally I focus on the key/mode of the piece that will be the focus of my practice. Since I'm currently focusing on the Koussevitzky Concerto, I do e scales and arpeggios first, and then normally just run through the rest of the minor scales just to get my ear used to the bass.
3) Ease into it. I don't start with the hard part. I pick a part that I'm reasonably comfortable with and get into the mood of the piece during that part. I also work on making that part sound better, but don't devote too much time to it, since there are parts that need more work.
4) Then I proceed to play the parts that need the most work and work on them. If I can't tell how best to improve the passage I set up my recorder and listen to it. I make notes on a whiteboard that I have in my practice space as I go.
5) I put the hard part in context. Depending on how far along with the piece I am overall, I will either just add it to the surrounding sections or the whole piece.
6) Run the whole thing, see if anything jumps out as needing work. If necessary repeat 4-5 with other sections.
7) Goof off for a bit to relax. I normally play some Led Zeppelin or Pink Floyd to mellow out after playing lots of hard stuff.

8) Take notes on what I want to work on the next day so that I don't forget.