Why should my opinions on this matter? I mean anyone could sit down learn about the exams and play "compare and contrast". So why keep on reading my thoughts? Well, you see, I've actually taken both exams so I'd like to think my opinion has greater weight. Someone on the faculty of either department can't sit down and tell you which they feel is easier to pass because they haven't taken both. It's a very different world taking the exams than what it is to make them up.
Before we get into that, though, let me take a few paragraphs to describe each exam so we have a common base.
The CIS Prelims are given once a year in January. The exam takes place across 3 days, with a 4 hour exam given each day. The exams covers 9 different subject areas that are either active research areas in the department or are considered to be "core" computer science by the department. 3 of these subjects appear on each exam. One exam is for "Systems" and consists of Architecture, Operating Systems and Networks. Another is for "Software" and has Compilers, Programming Languages and Artificial Intelligence. The last day is "Theory" and has Algorithms, Theory of Computation and Logic. When students take the exam, the ordering of the days may be different, but the areas are grouped in that way for every exam i.e., one day always has OS, Networks and Architecture on it.
The faculty are asked to write problems in a given area. 4 questions from each area are put onto the exam, for a total of 12 questions per day. Each question is worth 25 points. Students are asked to solve any 6 problems.
Two faculty members are asked to grade each problem. If their grades are different by more than a certain number of points they are asked to get together and reconcile the grades (I think the number is 5 points, but I'm not sure off the top of my head). The final grade assigned for a given problem is the average of the two grader's grades.
To unconditionally pass the exam, a student must earn a 70% on each day of the exam, not just 70% overall. Should a student be under the 70%, it's up to the faculty to decide what to do. If a student is close, the faculty may say "Take this class and get a B and we'll consider you passed for this day". Naturally, if a student is way under the 70% then they fail the day and there's nothing more to be done.
If a student fails the exam, then they have to take it again the following year. A student has 3 chances to pass the exam. If the student doesn't then they will be asked to leave the department with just a master's degree.
One other note about the exam. If a student fails one day, but passes the other two, then the student only needs to take the day he/she failed in the following year and not all three days. If the student fails two of the three days, then he/she must take all three the following year.
The Physics department's version is called the "Qualifier" or just "Quals" for short. The exam is given twice a year, once in January prior to the start of the spring semester and again in August prior to the fall semester. Similar to the CIS exam, the quals take place across 3 days, with a 4 hour exam being given each day. The exam covers only 6 areas, Electricity and Magnetism (EM), Quantum Mechanics (QM), Modern Physics (MP), Math Methods (MM), Classical Mechanics (CM), and Thermodynamics and Statistical Mechanics (TS). While only covering 6 areas, the quals actually cover more courses, as QM covers 3 courses and EM, MM, and TS each cover 2 courses. That makes for a total of 11 courses the student is to know.
There is no clear division of the days of the quals. Thus, one time MM and QM may be on one day and on the next exam, QM and EM may be on the same day.
Each of the 6 areas gets 4 problems placed on the exam. The qualifier committee solicits questions from the faculty and then decides which problems to put on the exam. In all, there are 24 total problems, with 8 being on each day. Each problem is graded on a 10 point scale. Two faculty are asked to grade each problem. If their grades are differ by two, or more, points, then they are asked to reconcile. If they can't, then a third grader may be brought in. The final grade for each problem is the average of the two grades. To pass a student has to get 50% overall.
Alright, so we've gotten all that laid out. Now it's time to compare and contrast the two. While the previous two sections were factual as far I know, this one (obviously) involves my opinion. If you've got a different one, then I'd be interested in hearing it.
So how does one compare these two exams? They cover entirely different areas and the difficulties of each can't be laid out in any quantitative way. The physics exam covers fewer areas, but more courses. The CIS exam has a higher plateau for passing. There's just no quantitative way of laying out the differences. So I'll give qualitative a shot.
In my opinion, the CIS prelim exam is harder to pass material wise. That may sound surprising given that the physics qualifiers cover 11 courses. However, there is a lot overlap in those courses. Material from Math Methods appears everywhere. Lots of material in Modern gets covered in Quantum and also Thermo/Stat Mech. Material on special functions, like spherical harmonics, appears in lots of places. Don't get me wrong, there's still a lot of material covered by this exam, but it's not quite as bad as if you had 11 completely separate courses. Contrast this with computer science, where this is very little overlap between the 9 courses. The process of resolution appears in both AI and Logic, but from what I saw studying for the prelims, the Logic way is slightly different and more involved. Thus, it's not a lot of overlap. Furthermore, resolution is usually asked as part of Logic, but almost never is it seen in the AI section of the prelims (I don't recall seeing it on any of the previous exams I had looked at, but I only went back about 3 years). Another very slight overlap is between Compilers and Architecture when talking about loop optimizations, specifically loop unrolling. But again, that's usually only asked about on Architecture section of the prelims and not on the compilers section. The last overlap, and the largest, is between Compilers and Programming Languages. The two areas have a lot in common, as PL deals with the study of features of programming languages, and the design decisions and trade offs those features involve. Compilers involves the study of how you get those features implemented. My opinion is that two sections could probably be combined into one without a problem. Nonetheless, the overall effect is that CS exam winds up covering more material than the physics exam.
Now having read the previous paragraph, one might be tempted to think that the CS exam is just harder. Well, it's not that easy. As with all good things in computer science, there are trade offs involved. The CIS prelims may cover more material, but the exam is overall easier to pass. Now I see you scratching your head at this admission since the physics qualifiers require 50% overall whereas the CIS prelims require 70% each day. The difference lies in the each department's rules about administering the tests. The CIS department gives its grad students more advantages to pass. Ok, it's 70% to pass each day. However, if you pass 2/3 days, you don't need to take those 2 days again. There is no such advantage in physics. If you get 50% on the first 2 days, but 10% on the last one, then you'll likely to be taking all three days again next time. Thus, for CIS, it's perfectly legitimate to spend a lot of time studying for two of the days and make sure you pass them and then take a shot at the third (perhaps you haven't taken the classes yet). If you don't get it, fine. Next year you can spend all your time studying for only that day. (In fact, this is the strategy I used to get through it. I only wound up with about 2 weeks to study for the exam, and had never taken Logic and only sat in on Algorithms, so I concentrated on the first two days and wrote off Theory day. I did look at the material and made sure I knew resolution from Logic and the topics on theory of computation, but I wasn't hopeful. I figured I could pass the first two days, and if I happened to get some theory problems I knew I may pass, but I could always just take theory day again next year. Turns out I got one resolution question and 4 theory questions that I could put down mostly right answers for. I wound up passing all 3 days on the first shot.) Furthermore, the prelims give you a total of 12 questions on each day and tell you to go answer 6. You can completely ignore one area if you happen to be strong in another area and know something from a second. Even better, the prelim questions very often come from the person who taught the relevant course last. Get a hold of the final from that class and you've got a fair idea of what could be on the exam.
Physics on the other hand gives you 4 problems in each area and tell you to get a 50% overall. You could take the view that you only have to answer 2 questions from each area. However, the qualifiers problems very often come from people who have not taught the relevant questions. So you can wind up in a position where the questions do not match what a particular professor covered when you took the course. It's quite possible that you could get questions that you have never heard about before. So it's in your best interest to answer as many as you possibly can on each day.
To wrap this up, the physics qualifier exam can be easier in terms of general material to know than is the CIS prelim exam, but CIS exam is easier to pass overall.