bburesh, I agree with the others in that Rome sneaks up on you and you keep finding more to see with every turn - but if you're limited in time, and don't want to subtract a day from another city (although 3 days in Munich will still allow for sightseeing and the Castles), you could do something like this:
Day 1:The Vatican - this includes the
Vatican Museums (with the
Sistine Chapel - opens at 10am but get there by 8.30/9am to line up to ensure you get in) and
St Peter's Basillica (in the church, down in the crypt and wander the square). You could also climb the
Cupola (dome) if it's a fine day and you have time, or leave it for another day as you'll be Vaticaned-out by the end of the church and museums. Don't worry, there's a lift for part of the way and the views are worth it - especially into the Pope's back yard! Access is from 8am until 4.45pm so slot it in to your day accordingly.
Day 2:Colosseum & the Roman Forum - buy your ticket at the Palantine Hill ticket office (just up the road) as it's quieter and quicker, then you can just wander in to the Colosseum without waiting in line. Spend time in the Colosseum (see what's on display in the museum section - there was a Gladiator exhibition of artefacts found in the arena) then wander over through the Roman Forum (it's free), under the small olive grove and sample the water coming from the pipe (a Roman Nose - check the shape!) in the Forum that still feeds water to anyone who want to collect it there.
Once you've finished in the Forum, wander up inside the
Vittorio Emanuele II monument in Piazza Venezia for great views over the city.
Have lunch in a pizzeria ("Fornaio" or "Pizza al Taglia" are signs to look for) or paninoteca (sandwich shop - but what sandwiches!) somewhere in the side streets to rest your feet.
Capuchin Crypt at Santa Maria della Concezione church (Crypt open: 9-12noon and 3-6pm); located in via Veneto just off Piazza Baberini (Metro stop of the same same); leave a Euro1 or 2 donation at the door and pay your respects to the bones of over 4000 capuchin monks that have been used to "decorate" the crypt - look for the eerie sign at the end.
From here, you could make a
passagiata (slow stroll - very Italian) as it should be late afternoon. Start at Piazza Baberini (outside the Capuchin Monks) and walk down the hill to the the
Trevi Fountain (main road is via del Tritone). Spend time here (a great gelateria called San Crispino is in a street two back from the fountain) before continuing to the
Pantheon (it closes at 7pm so get there beforehand to go inside - amazing structure!) and finishing in
Piazza Navona (three great fountains and art for sale - just watch the pickpockets). Have dinner in one of the great
trattorie in the streets surrounding the square (just walk one block off the square for local food). If you can still walk (!) see if you can make it over to
Castel San'Angelo (about 15mins through the back streets) when it's lit up and look up the street that leads to St Peter's for an awe-inspiring view. This depends on where you're staying, but there are busses (#40 will get you back to Piazza Venezia, eg) that you can take from next to Castel San'Angelo to either a Metro stop, Termini or your accommodation.
Day 3:After your feet have recovered (you haven't "done" Rome unless your feet ache!), make your way to
Piazza del Popolo and go inside
Santa Maria del Popolo church to see the two amazing, and hidden, paintings by Caravaggio (the only concession you have to make to "art" if you want, but truly worth a quick stop).
From here, wander down
via del Corso for a bit of (window) shopping before arriving back in Piazza Venezia. Wander up the slight hill that runs along the right of the Vittorio Emanuele monument (away from Piazza Venezia) and visit the
Mouth of Truth (Bocca della Verita). It's located in the small courtyard at the front of
Santa Maria in Cosmedin (church). You might recognise it from the movie "Roman Holiday".
Then walk across the road to look at the remains of
Foro Boario - the two
Temples of Portuno (Portunus was a Roman god of keys and doors) and
Ercole (often referred to as the Temple of Vesta as it is similar in shape to the original in the Roman Forum).
From here, face the river and turn left to walk to Piazza dei Cavalieri di Malta (square of the Knights of Malta) to find the "
Keyhole of Rome". There's a large green door that has a key hole in it and if you look through it you'll get a great, and different, view of Rome. The views from the Orange Garden (Parco Savello or the Giardino degli Aranci) just near it are also spectacular, especially at sunset. It's not a "must do", but it's something different for you and doesn't involve a museum.
After than, you can walk up around the road to
Circus Maximus (Circo Massimo) to see where the chariot races used to occur (now home to joggers and large city concerts). From here, you can either take the Metro (it's all about saving your feet!) at the end of the road near the Caracalla Baths (these are also worth a visit if you're interested and have time) to your next destination - whatever that may be.
As far as museums in Rome go, it's not like Paris with the Louvre, Musee d'Orsay, Rodin, l'Orangerie, etc. But, there are still things to see that you might consider "museums" so do a little research (but I suspect you already have) on the above to see that they fit your criteria. There are plenty more (Nero's Golden House, the Catacombes, Villa Borghese), but these are a good start.
I notice that at the moment, you're in Rome in the middle of the week, which means you won't have to worry about getting in to the Vatican Museums (Sistine Chapel) on a Saturday or them being shut on a Sunday. If you want to make absolutely sure of your times and days (and no sneaky public/Roman holidays) then look at
www.vatican.va and check their 2007 calendar. The schedule I've written is just a suggestion - by no means let it limit you as to what you want to see. It's a good way to cover a lot of things in a little time, but remember that you'll be on the go just to see it all in 3 days.
Happy travels and remember - a bidet is also a foot spa!
EDIT: as you'll be there in May, the Spanish Steps should be covered in azalea bushes in pots - the only month they are worth visiting and look like they do in post cards. Slot in a 10min visit either when you're walking from Barberini to the Trevi Fountain, or when you're in Piazza del Popolo.
