Somerville, MA fits the bill pretty well, for sufficiently small values of "decent climate".
I liked the boat house, in the Charles river, were you could register for $120/year, and learn how to sail. The urban transport is pretty good (better than bay area).
For me it was good for a year or two, and then it ended up being boring. Moved to SF, and my quality of life improved a lot. people are just way much friendlier in here.
edit. there are a lot of biotech jobs around there (in Cambridge mostly). Lot's of tech jobs, but it is mostly big coorporations, and nothing too exiting. Few startups, but no near the number of startups in SF bay area. But housing is cheaper, about %30 cheaper, but still very expensive (third most expensive area, after NYC, and SF). And you can meet lot's of smart people, with masters, phd's, etc. More intellectual than the bay area.
Boston is interesting in that population density declines pretty sharply as you move away from the city center. So Boston itself has a population of 600k and skyscrapers, Cambridge has 100k and still feels fairly urban, Arlington and Lexington each have about 40k people and feel like large towns, Bedford and Concord have 15k apiece and feel like small towns, and Carlisle has 4k and feels positively rural. I'm on an acre of land in Bedford, with woods in the back, and only 13 miles outside of Boston.
The northwest suburbs also don't lack cultural activities the way many suburbs do. You've got all the historical sites in Lexington, Bedford, and Concord; the Lexington symphony orchestra; community activities; libraries in each town; band concerts; fireworks displays on July 4; etc. I was going to say "Flipside is that you need a car to get to them," but even that's not really true: a bike path connects the town centers of Bedford, Lexington, Arlington, and the Alewife subway station in Cambridge.
Only problem is that property values are sky-high here, though they seem to be going down fast. The house across the street went on the market for a million, but finally sold for $630k six months later. Houses are still going for $1M+ in Concord and Carlisle.
Well, that and the "sufficiently small values of 'decent climate'". The cold & snow isn't as oppressive in more rural settings though; it's quite pretty out now.
There's also Middletown, CT and New Haven, CT, both of which I've lived in. Middletown's a neat small city with Wesleyan University in town and a cool small downtown, classic New England. Anywhere in the Connecticut outback is a likely spot for some biotech, Bayer and others are big in the state.
New Haven was really ugly 15 years ago but now it's largely an awesome residential city; you want to live in the "grad ghetto" with all the Yalies. Cheap housing, great restaurants, cool up-and-coming atmosphere. I loved the year I spent there. The downside is schools - if you have kids you should send them to private school.
I don't know about the biotech scene, but I love visiting Portland, ME. Anybody able to speak to that city? Another great medium-sized New England town.
But there are a number of tech companies around, either in Cambridge/Somerville or in the Boston suburbs. The public transportation system is decent and the city is compact enough that a lot of things are within a half-hour drive of one another.
Regarding biotech, I used to work on the Human Genome Project at what is now the Broad Institute (which got spun off from the Whitehead Institute). Novartis rents a floor or two of the building I work in and owns a whole building a block away.
Boston's Museum of Science is a good place to take kids; they have a "Discovery Center" that's specifically oriented towards 0-to-5-year-olds, but my three- and five-year-old have fun at a lot of the other exhibits as well.
I currently live in Providence, RI which is about an hour south of Boston. Smaller hacker community, but at least there is one and its not to far from Boston either. We also have a growing BioTech industry thanks to Brown University. I have a friend that works at EpiVax and loves his job. Might be worth checking out.
We moved to California from Providence. The * best * assortment of restaurants in the whole country, as far as I'm concerned. The Boston Globe often says that 9 out of the 10 best restaurants in Boston are in Providence. Good entertainment scene, arts scene, etc...
Downsides: The townies (locals) get a little crusty, and you have to get used to the idea of government == corrupt.
We moved to LA so my wife could try out the film scene, and because my contract work in health care was drying up fast.
The winter's do get kind of long, though. And if you hear people talking about a coming, "Noreestah" go to the store and buy all the bread and milk you can. :)
If you do move to Providence, be sure that you live on the East Side of town. It can be really hard to make friends if you're living anywhere else. The native Rhode Islandics aren't really used to people from anywhere else, and it takes a long time to make any headway in the friends department. The East Side has RISD and Brown, so people on that side of town are a lot friendlier and used to strangers and "ethnic people". (My landlord's phrase, not mine. Ironic because he was very Irish. :D ).
Heck, anywhere in New England is pretty nice, and you can drive from one state to another in less than an hour. It's all pretty close.