We've done two so far - a short one and a long one.
The short one - good for a weekend - take the train to Gebze and then the ferry over the water. Follow the Marmara east for 7 km and you'll come to Karamursel (or Altinova? don't remember, check a map): turn south and go to Iznik. It's 65 km on quiet lovely roads (except for the first 7 km, and that's a highway that isn't too busy and that has a good shoulder).
Iznik is a little expensive for hotels, and the cheapest place - which, sadly, also looks like the prettiest place - won't let Turk/yabanci couples stay unless they're married. Generally hotels cost about 70 lira for two people.
You can come back the same way, or there are two other options -
1. Follow Iznik lake west until you come to Orhangazi and the main highway, and then go down the highway to Yalova. The Iznik lake road is nice but the highway is TERRIBLE - it's downhill, but the shoulders are narrow and traffic is heavy.
2. Go east out of Iznik and head for Adapazari. You can get buses back to Istanbul from there, or you can take the train. Beware of taking the train on Sunday evening, though: it gets crowded and you'll probably have to sit in the luggage van. Iznik to Adapazari is 88 km. The road is in three sections. From Iznik to the highway is lovely - gentle rolls uphill and then an exhill-erating downhill (pun intended). The second section is a long run on the highway next to the train tracks - easy but not very pleasant as traffic is noisy. Then the road cuts downhill through a valley to Adapazari. It's a beautiful valley but traffic is heavy on this road.
Overall, I'd recommend returning to Iznik on the same road you came in on.
The other trip we did was Istanbul - Soma. (Soma is near Bergama). Tips:
1. Get out of Istanbul early in the morning, and get the highway from Yalova behind you. Once you turn off on the road to life gets much better.
2. You will never have to pay for tea in Anatolian villages, provided you are friendly.
3. Sheepdogs and dogs in general in Anatolia are not used to bikes, and will chase you. THey are generally friendly though, so if you stop and talk to them you'll be fine. But use your judgement as to when you should pedal hard!
4. Cesmes are no problem anywhere. Take a big bottle and you'll be fine.
5. Big buses will happily take your bike, bunging it in the luggage compartment for no fee. (Well, I've only experienced two big buses, but so far so good!). Minibuses may take your bike but you might have to pay, dismantle it, beg, or whatever.
6. Anatolia's winds are stronger than you would expect.
7. Turkish drivers are a LOT better than I expected them to be. Istanbul drivers suck but once I was out in the countryside I never once felt that a truck or bus had passed me too close.
8. Old men can always give you a reliable idea of distances and hills, because they probably walked the area in their youth. Young modern people have probably only ever driven the area, so they'll have no idea.
9. In Istanbul, drivers and pedestrians alike see bikes as pedestrians. If you take up a car-space in traffic, even if you're going at the same speed, drivers get indignant. But in small towns it's different - people are more used to seeing bikes as traffic.
10. Most importantly - take TONNES of sunblock and don't forget your toes, ears, scalp, and lips!