After poring over maps and reading up about Orkney beforehand Stromness seemed the ideal base as it was closer to all the monuments at the ness and skara brae etc than Kirkwall and also good if you want to get the ferry over to hoy.
You're probably right, a bike would be a good idea!

I was doing some recording while I was there and it was easier for me to be on that side of the mainland.

We'd taken a car up with us so I can't advise on public transport, but I'd advise hiring a car if you do stay in Stromness and want to get down to South Ronaldsay to see the tomb of the eagles or banks (the latter I strongly advise visiting).
Having the car made getting to the monuments very easy, I imagine it'd be a struggle to get round to a lot of them without one (Wideford for example), but not impossible.

We went to Kirkwall on one of the days and had a nice meal there in the evening. It's much bigger than Stromness, more shops etc and definitely worth a visit.

I suppose it depends on your priorities but I'd advise Stromness as the best option simply because of it's proximity to the ness (brodgar, maes howe, stenness, unstan, barnhouse etc). It meant that we drove past those monuments many times on trips out and therefore saw them in all sorts of light and weather.
Great for photography.
I remember we were driving back to Stromness one afternoon and when we got to near the ness there was a fog rolling in over the ring of brodgar, but the sun was also shining brightly, illuminating it. i'd never seen anything like it in my life. Brodgar was shrouded in some sort of otherworldly glowing mist, it was a bit of a 'moment'! I stopped the car and got out and just stood there taking it all in. Will never forget that.

Wherever you stay you can't go too wrong, and i'm sure you'll have a fantastic time.
Orkney really is a magical place.

ps. Check out the Hamnavoe in Stromness, we had a really lovely meal there. A tiny little place tucked away up a side street. Make sure you phone ahead as it gets booked up quickly.

I'd agree with tjj and Evergreen that Stromness is your most convenient stop for the best sites. I stayed at The Ferry Inn last year. It was okay, nothing more - they weren't very flexible with Shetland ferry arrival times (when I was refused a drink at the bar at 11pm) or with early ones either (I had to miss out on breakfast on my last day) and that, with a very indifferent evening meal in the bar, made for a shall we say compromised experience. On my previous visit I stayed at the Stromness Hotel which was more expensive but worth the extra cost, especially if you can get one of the front facing rooms: excellent views. If you can afford it, I recommend staying there.

Kirkwall is a nice town with plenty of good bars to keep you busy in the eve, but the hotels are dearer.

We stayed in a couple of nice places.

If you go to the page of a site you want to be near - eg Ring of Brodgar http://www.themodernantiquarian.com/site/388/ring_of_brodgar.html - there's a dropdown for "Facilities".

On that page you'll find a few recommendations. :)

Mine are Lochend (with views of the Stones of Stenness and Maes Howe among other stuff) and Atlantis Cottages. We loved both. :)

G x

Maybe a bit of a luxury if you are pushed for time , but the cliff walk on Hoy is a cracker , the bonxies can be attentive .

I went to Orkney a few years back, flying into Inverness and hiring a car (picked up from airport) Drove up to Gill's Bay and caught the ferry over to the island staying at Finstown which was a good if not quite place. The car came in very handy and is a must for touring the various Mainland and South Ronaldsay sites especially if time is short.
I also visited Rousay and Eday taking the car with me. However it would have been nicer and easier (and cheaper I would imagine) to take a pushy. There are many sites to visit on these islands but all are easily to get to on a bike. Beware ferry times and days, if i remember it was a bit of a task organising myself to get to the islands in to the week I was there (on top of everywhere else i visited) as not all ferries operate all week. Kirkwall has plenty to see and do including the museum and St Magnus Church but if I did it again I would stay in Stromness. I continued with my journey in the car and drove to Ullapool and over to the Western Isles to visit Callanish and plenty of other places along the way. Hope to do it again one day it was a fantastic experience.

We went to the Orkneys for 5 days back in September last year by camper van. The advantage of this is that you can get to and stay near nearly all the sites you'll want to see without spending on B&Bs, hotels or unnecessary journeys (you can free camp just about anywhere in Scotland as long as you're not annoying anyone or trespassing). Camper vans can be hired for as few as 3 or 4 days if you can get your booking in early and I think if the van's not too big you can travel on most of the inter-island ferries, again pre-booking these.

A nice place to stop the night is the Brough of Birsay, right up in the NW of Mainland. It's not prehistoric (Pictish/Viking), but interesting and you can walk across to the tidal island at low tide to view the site. There's also a public toilet and shop in the nearby village.

Have a good'n!

I would recommend staying in Kirkwall.

It's pretty central on Mainland, only about 8 miles from the Ness of Brodgar/Stenness Maes Howe etc., and is closer to South Ronaldsay for Tomb of the Eagles. It also has by far a bigger range of places to eat & drink, and get supplies than Stromness, and if you wanted to visit some of the other islands the majority of inter-island ferry connections leave from Kirkwall harbour (only Hoy & Rousay sail from different terminal's).

Taking the car on inter-island ferries is expensive but there is cycle hire in Kirkwall, and it only costs you the fee for a foot passenger if you take the bike, you can see quite a bit of the the other islands by bicycle during a day trip, plus the roads on them are really quite! The travel/tourist information centre in Kirkwall has a leaflet with all of the ferry timetables which is useful if you are thinking of visiting the other islands.

There are no shortage of wonderful places to visit on Orkney so I'm sure you'll have a fantastic time wherever you go. If you are visiting during the summer though I'd suggest pre-booking a visit to Maes Howe as often it gets fully booked up due to block bookings by cruise ships, and Maes Howe is really not one of those places you want to miss!