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I was in Bali for my honeymoon last year around the same time in Nov 2011.

Here's what I recommend:

Hire a driver:
I cannot stress this enough!!!!!

We found our driver on Tripadvisor. Company name is The Bali Driver and Tour Guide. Didi is the owner of the company and we had him personally drive and give us a tour of the Bali for 3 days.
It's pretty good price as it's $40-$45 USD for a 8 hour day (including gas, parking, tolls) and plus whatever you want to tip. Without a driver it would be so hard to get around as I wouldn't trust getting into a cab in Bali.

I'm not saying it takes 3 days to tour the whole Bali but you want to spend some time in different areas. Also the roads are very congested there and the guys on cars and bikes drive like they are in another world. If you think Richmond on a Saturday afternoon is bad, wait till you see Bali!!!

The Areas:

Seminyak:
This is more of the beach resort side where you find really nice beaches and private villas. We ended up renting one here for about 5 days on a honeymoon package and it was great! Villa was a 1 Bedroom 1500+ sq ft with own pool.

I would definitely check out KUDETA (restaurant and beach club). It's fronted along the beach. Food and Sunsets there is AWESOME!!! and cannot be stressed. It's where all the Aussies go. Think about this place as the best beach restaurant club in KITS.

There's one main street in Seminyak, not far from KUDETA that is like the main drag (has all the restaurants (warungs fancy and normal), designer stores) worth checking out but nothing too too special.

Ubud: (45 mins to 1.5hr away from Seminyak)
I actually love this area the most. It features all the cultural, heritage and rural parts.

The rice paddie fields and all the greenery (jungles, forests, whatever) is amazing here!!!!

I would hit up that main wet market (I think this is pretty much the DT of Ubud) where you can buy all the trinkets, souvenirs and knick knacks. Next to the Ubud market is also this lotus temple place which is pretty historical and quite the scenic. The few streets around the area also features pretty cool local artist shops for different types of crafts.

The Roast Pig Place (Babu Galing) is located across from the Ubud market. It's the one and original one. There are other locations which I actually recommend those ones as its cleaner and more tourist orientated.

** Recommend to try the Bali Roast pig but it has nothing on Chinese Roast Pork. Don't want to spoil too much but try it and you'll know what I mean **

There is also a good ATV rental tour service here (3-4 hour tour) where you rent the ATV and go ATV in the rice paddy farmland and jungle.

Jimburan:
Famous beach area where you go for Seafood.
Go here for dinner in a restaurant near the middle or whatever is recommend. You literally sit on the beach, beach side, enjoy the seafood dinner and sunsets.

Historical Sites:
I went to quite a few including Monkey Forest, this temple the north west point of Bali, Elephant Cave, the Volcano, war musuem but all in all they were all MEH for me. So YMMV if you like that kinda stuff

Local Art (Silk making, silver and wood crafting)
It's quite famous there and I recommend to visit the crafting estates (owned by a family that specializes in one of the crafts) and see if you wanna pick up and buy anything yourself.

MUST READ TIPS!!!!!! (Cannot stress enough)
- Make sure you are current on all your vaccines (check with your doctor)
- Watch out for Bali Belly (Traveler's Diarrhea) bring your medicine or get vaccinated. Drink only bottled water and don't trip the tap water. We were very careful (washing hands and watching what we eat) and both ended up getting the runs the whole trip. My wife had it the worst and I ended up not to far from her.
- HIRE A DRIVER (worth the money spent on it - read above)
- Safeguard your passport, money, valuables. Leave money in your hotel safe. Have 2 wallets when you go out or split up the money thats on you
- Observe and respect Balinese tradition and religions (Balinese people are very religious and you'll see alot of it when you are in Bali)

RECOMMENDATIONS:
- KUDETA for sunset with pizza and beers
- ATV'ing @ UBUD
- Visit a coffee plantation (try the Cat Shit coffee) and see the rice paddies located past UBUD
- Eat at Naughty Nuri's @ UBUD. I'm still salivating from there charcoaled pork ribs
- Try the Babu Galing (Balinese Roast Pork). Lots of locations.
- Try Teabolee (herbal teal like soft drink)
- MUST eat Rotiboy (franchise bakery that sells the most fresh and best crispy sweet bun - kinda like a chinese mexican bun)
- Try KOLEGA (clean Balinese home styled food in a cafeteria setting its in Seminyak)

One small observation:
It's unfortunate but the locals have preferential treatment and kickbacks as tourism is a predominate industry in Bali.
- At the Babu Galing place in UBUD they have the menu with no prices. Tourists pay the higher price while local taxi drivers pay the local price. You get the same amount of food.
- It's notorious for drivers to get commission and kickback from the money you spend at the places they bring you (artist factory, restaurants)

Hope this helps with the very long post. Let me know if you got any questions!