Planning my Oxford Itinerary - "Must-see" Sights versus avoidable ones?

It depends on whether some of the things you've mentioned are just to see from the outside or to visit properly. You shouldn't count on being able to get into colleges as they're working educational institutions and not tourist attractions. September is still in the summer vacation but they often have conferences and so forth going on. You have a better chance of getting in if you dress for business and don't look like a tourist, but if you're stopped don't waste everyone's time arguing. Similarly the only part of the Bodleian that is open to the general public is exhibition space, which for me depends a lot on what is on show at the time you go - there are regular themed exhibitions. You will definitely not be able to get inside the Radcliffe Camera and probably not the Sheldonian. The Clarendon Building is entirely private offices.

The absolute musts on your list for me would be the Pitt-Rivers, and Ashmolean. The Natural History Museum is in the same building as the Pitt-Rivers, and you will actually have to walk through it to get to the Pitt-Rivers.

I've never been to Blenheim, but I think it may take more than just a morning. Your day three is seriously, seriously rushed.

Very heavy on the 'tourist' Oxford: perfectly understandable, but worth pointing out. Try going down the Cowley Road as far as you feel happy with for a different perspective. Plenty of different places to eat down there ... plus the Ultimate Picture Palace.

Also don't neglect the quiet charm of The Parks.

Also agree day 3 is over packed for my taste.

Some of your must-dos are just quick walk-throughs and others will require more time...
Bodleian Library - the only way to see it is to take a tour - or become a visiting scholar :). Tour is 60 - 90 minutes long but well worth it!
Blenheim Palace - I've been out there by public bus and it takes longer than you might think to do it this way. There are stops along the way and the bus drops you on the main road that runs by the palace, not directly at it. You have to walk from the main road all the way to the palace...at least 20 minutes. It doesn't open until 9. Tour is around 90 minutes long or so. You'll also want to walk around the gardens to the back of the palace. I wouldn't plan on less than 5 hours from the time you get on the bus in Oxford to the time you get off again.
Day 3 just isn't possible...Blenheim + 2 museums in one day really isn't realistic. Consider switching out the Ashmolean with Blackwell's, which is open till around 6-6:30 I think. That might give you a little more wiggle room with your time.
For most of the colleges that are open to the public you can just walk in (some with a fee) but for Christ Church, they have a prescribed route you have to follow - allow for at least 40 minutes if you keep moving.

Hey all, thanks for the advice! I'll keep it in mind and swap around my list accordingly.

By the way, could anyone give a rough gauge on how long does it take to explore the colleges (christ church and magdalen) / museums / Botanic Gardens? I think if I had an idea of the time I would be spending at each location it would be easier to plan the schedule around it. (Thanks for Bodleian and Blenheim, anita.)

Christ Church...at least 40 minutes
Magdalen...30 minutes is really all you need - it isn't big and there aren't too many buildings you can go into...just the grounds, which are perfectly kept, and over to look at their deer park.
Ashmolean - it isn't huge but it isn't small either. It is one of those museums that has an "overview" collection. It doesn't focus on just one thing...it has a smattering of everything from the ancient to the modern. I would give it about 1.5 - 2 hours if you don't linger anywhere too long. The rotating exhibitions are in the basement...how long you spend there will determine if you're interested in what is on display or not.
Botanic Gardens - You can walk through the whole thing in 20 - 30 minutes...they are right across the street from Magdalen College so you can easily pair these two.
I don't know if you are interested in literature or not but I don't see The Eagle and Child Pub on your list. CS Lewis and JRR Tolkien used to hang out here together and edit each other's work...it's a nice place to go for dinner or a drink in the evening. There are some nice artifacts of the two on the walls.

Day 3...Ashmoleum Museum.

Yes, the Ashmoeum. And after the museum stroll across the street to the McDonald Randolph Hotel for a drink at the Morse Bar if you are a fan of the Inspector Morse shows.
http://www.macdonaldhotels.co.uk/our-hotels/macdonald-randolph-hotel/eat-drink/the-morse-bar/

The Morse Bar is somewhat of an icon in Oxford city. Often frequented
by actors and politicians, the bar is classically decorated and exudes
elegance.

Its popularity extends to the patronage our most famous resident and
the bar's namesake, Inspector Morse; a frequent setting for many
scenes where Morse and Lewis have deliberated on complex cases.

The Morse Bar still features regularly in episodes of the follow-on TV
series, Lewis.

At night, no plans yet.

Try the historic Turf Tavern for pub food, drink and atmosphere. A bit hard to find. If it were a stranger taking us there through the dark alleys instead of an Oxfordshire friend I would have expected to be mugged.
http://www.theturftavern.co.uk

http://en.wikipedia.org/wiki/Turf_Tavern

The Turf Tavern (or just "The Turf") is a popular but well-hidden
historic pub in central Oxford, England. Its foundations date from the
13th century and the low beamed front bar area from the 17th. It was
originally called the Spotted Cow but changed its name in 1842,
probably as a reaction to gambling meetings held on site.

The Randolph is being a bit naughty with the Morse connection - in the novels and most of the TV shows his favoured pub is the White Horse, which is between the two original buildings of Blackwells on Broad Street.