How much time to allow for these Rome museums?

My experience with tours is that they give you a summary and take you to the highlights of the site. We did the RS guidebook (downloaded it into our Ipod) tour of the Colosseo and the Forum and that took about 3 hours and that didn't include Palatine Hill because we were ready for a break after that. We did an escorted tour of the Vatican/Sistine Chapel that took about 2 1/2 hours. We walked thru the Gallery of Maps/Tapestries that ended at the Sistine Chapel (you know that it's about a 1/4 of a mile walk from the Vatican Museum entrance to the Sistine Chapel thru those galleries). From the Sistine Chapel, there's a tour group exit (it's in the RS book) that's a shortcut to St Peter's Basilica. From that area you have a choice of: going into the basilica, going down into the crypt (free, takes about 10-15 minutes) or taking the elevator up to the cupola (definitely recommend that, don't think any guided tour takes you up there, costs E7, if I remember right, did it last month). If you're part of a tour group, I don't see how you can't just break away at any part of the tour or stay extra at the end, after all you already paid for the admission. As for how much time to allow after the tour is over, that is entirely up to you, your will, and your endurance! PM me if you have any questions.

With the Colosseum/Forum/Palatine Hill tour, your will actually be entering two separate ticketed areas. You would be able to linger in whichever area you are after your tour ends, but you might not be able to re-enter the other site. FYI - the Forum and Palatine Hill are connected and can be accessed as one entry; the Colosseum is separate. I thought RS's Forum self tour was very good. For my money, I'd do that one on my own and only get a guided tour of the Colosseum.

We did the Coloseum/Palatine/ Forum in one day. Got there fairly early at the Coloseum and was booted out at closing time at the Forum. I like to take my time so you could do it quicker and still get the highlites of everything. I would've taken more time if I could've.
The Vatican.....forget it......the museum is huge and with all the other things.....do research and figure what you want to see the most. We spent a full day and saw only a portion of everything.

Can't help with the first three - all the times I've been to Rome, and haven't been to those museums (yet). One time we visited the Vatican Museums with the guided tour offered through the Vatican; about 2 hours, and ending in the Sistine Chapel. It was informative, but I felt very rushed. So on the next trip, we did it ourselves, using Rick Steves and the "Blue Guide," which is very detailed and quite dry. I think we were in the Vatican Museums for about 2 1/2 - 3 hours. Our focuses were paintings and sculpture. I much preferred visiting at our own speed. We spent a LONG time in front of the Raphaels. On one trip to the Colosseum/Forum/Palatine, we took a guided tour by Context tours, a very good company with very knowledgeable guides, but quite expensive. I did this primarily because the Palatine area is so ruinous; it was very interesting and helpful for the Palatine area. Less helpful for the other two areas, which we had visited several times previously. The guided tour was about 3 hours, I think. The Colosseum and Forum by themselves, maybe 2 hours total.

Burton, a lot depends on how important the relevant type of art is to you. I've been through the Vatican Museums many times and still can spend more than a day there on each trip. Three hours would be minimum time... I'd guess it would take 20-40 minutes (depending on crowds) to simply walk from the museum entrance to the Sistine Chapel without looking at any of the art along the way.
I made it to the Galleria Doria Pamphilji for the first time recently and really enjoyed it. One could easily do it in a couple of hours, maybe 4 hours if you want to linger with the art or spend more time with the building itself.

On our third visit to Rome we finally made it to Galleria Doria Pamphilj and really enjoyed it. It is cool, relaxing and offered a different side to Rome by touring an aristocrat's home and learning about society and art. We did have to wait for the audio sets but I would allow two to three hours. The audio sets allow you to control the depth of your tour by pushing additional options.

Thanks to all for your replies to a very subjective question. In the end, the amount of time to allocate will probably come down to a balance between my lingering and my wife's tolerance. When I was last in Rome, as a backpacking, hosteling teen in 1976, I remember spending an entire day hanging out (including the now forbidden picnic lunch) in the forum and on the hill. I also spent the better part of a day at the Vatican. But my wife, who has never been to Rome, tells me that she spent 2 to 3 hours in the Louvre her first time in Paris and, while she has been back to Paris a time or two, has not returned to the Louvre. Locally, she tends to be waiting for me at the end of museum visits, while I am doubling back to further linger over a favorite painting or two.... Compounding the scheduling issue is our limited 3.5 days in Rome. I doubt we can see all the museums listed in my original post without rushing from place to place, which neither of us enjoys. I expect it will be 2.5 to 3.5 hour visits to some of the listed sights, with equal time wandering the streets and eating gelato. So, here is a different spin on the question: If the Vatican, Colosseum/Forum, and Borghese are at the top of our list, and we have time for one other 3+ hour attraction (not things like Trevi, Navona, Spanish Steps), what should it be? Galleria Doria Pamphilj, Galleria Nazionale d'Arte Moderna, Musei Capitolini, or something else?

Burton, I'd recommend the Galleria Doria Pamphilj. I did it with someone who, like your wife, tends to move through museums relatively quickly. They enjoyed the residential aspect of the museum, and there's a nice cafe by the exit where they enjoyed a coffee/pastry while waiting for me. And there were some lovely pieces in the collection.

We attended a concert at the Doria Pamp and it was a package deal with seeing the museum before the concert. IMO an hour and a half is plenty for the museum. Agree that the Vatican can be an all day experience. I think the Borghese is a timed entry of two hours. Save time for seeing the wonderful churches and wandering lots of tiny sidestreets. It is entirely possible to overdose on museums-with their crowds.