I have two different types of practice -the daily one (which, depending on my household obligations, can run from half an hour to an hour), and my weekend practices, which run 3 to 4 hours each (or more) on Saturdays and Sundays.
In both cases I start with a song list. I begin warming up with some Porcupine Tree (PT) stuff.
If it's a weekday daily practice, I'll finish about 2 or 3 shorter fun PT songs and then switch to our bands newest originals and newest covers, or learn them (depending on if the song is still being written or learned). That's usually all the time I have on weekdays, and that's the critical stuff.
For weekend long practices, I start off with PT then go to Rush or ELP, and get progressively more difficult until I hit the Dream Theater/Liquid Tension stuff, and then I go through my band's originals, then go back over the very difficult stuff in sections, repeating the hard stuff over and over (sometimes slowing stuff down with an app I use called iRehearse and repeating it a dozen times slowly), play through the most difficult sections/riffs, anything that didn't go smoothly during the practice to that point. For instance, this past weekends 'most difficult stuff' was an original with a four-finger right hand finger picking intro and Dream Theater's Metropolis Part I, going over and over the bass solo, and the section immediately following the guitar/keyboard solo (riding that F#!) until the end.
I don't really go over scales or anything very often (unless I'm playing something in a song and I want to try an easier fingering). I do go over techniques like tapping and chording in between songs, or if I'm finishing up a weekend practice and noodling around a bit. I will sometimes put on a drum track and jam along just for the fun of it, but that's it.
I also record all of my practices and rehearsals with my bands through an iRig into my iPhone and listen back later to see what I'm doing - what works and what doesn't. I'll often take something I'm hearing there and work on it during a weekend practice, or, if it's short and critical, a weekday rehearsal where time is tight.
I'm sure my practice routines could be improved upon enormously with a more disciplined approach to practice (scales, etc.), it's just that I have limited time and a lot of difficult material to cover, so I have to make choices as to what to work on, and I'd rather spend my time working on a difficult part to a difficult song.