I've been following the Rippetoe protocol where you squat before you deadlift. Would it be ok to deadlift beforehand? By the time I get to deadlifts, I'm so tired that I can't lift as heavy. Or does doing squats first the best way to increase strength gains?
Generally squats are done first as they are the better all around strength builder and they warm you up for deadlifts. That being said, once you get more advanced if you are trying to build a better deadlift you can prioritize it, but for the average lifter they will be better off doing squats first.
If you are doing Rip's program, the just do the program. If you're adding weight, then the right stuff is happening, regardless if you're tired. Plus, it's working out, you're working out, it ain't supposed to be easy.
Hey JB,
Despite the popularity of the various 5x5 programs, there is nothing magic or special about them. If you find that you feel better doing your DL first, do it first. There is also no reason why you must squat all the time. There are 100's if not thousands of ways to set up a program.
Personally I prefer the DL over the squat for total body strength. If I had to pick one (which I don't) I would choose the DL.
Let me know if you would like some examples.
TAKU
Personally I always do squats before deadlifts. Deadlifts wear me out and psychologically I want to be at full strength when doing squats because I hate the idea needing a spotter for squats.
Why not do them on different days to get the most out of each? 
future_jabroni - Personally I always do squats before deadlifts. Deadlifts wear me out and psychologically I want to be at full strength when doing squats because I hate the idea needing a spotter for squats.If you don't need a spotter when squatting your doing it wrong
When i did starting strength, i would deadlift about 3-4 hours after the rest of the workout. 
OregonChaelClosedDueToBandWagonCrash -future_jabroni - Personally I always do squats before deadlifts. Deadlifts wear me out and psychologically I want to be at full strength when doing squats because I hate the idea needing a spotter for squats.If you don't need a spotter when squatting your doing it wrong
I must be doing it wrong then.
@Taku
Yes, I would love some examples!
OregonChaelClosedDueToBandWagonCrash -future_jabroni - Personally I always do squats before deadlifts. Deadlifts wear me out and psychologically I want to be at full strength when doing squats because I hate the idea needing a spotter for squats.If you don't need a spotter when squatting your doing it wrong
I hear ya'.
I tried deadlifts on a different day than squats and felt knee pain almost immediately. Squats really do warm you up well. I'm still trying to figure out the same balance as you, i'm usually really tired by the time I get to deadlifts. And I don't think being exhausted from a workout for a couple of days is the point of fitness.