I have a 2004 Cooper, 5spd manual. It is an unbelievable car, very chuckable, quick, always brings a smile to my face. Never left me stranded, regular maintanence plus one random problem. This was a steering rack that went- the seal leaked all of the fluid; however this was after driving from NH to Chicago in a blizzard through Indiana with lots of snow/ice and the low ground clearance of the Cooper. I have just over 65k amazing miles on him now.
For the first gen, the 2005-2006 models are your best bets. The Cooper S for those years is supercharged and the whale from it as it spools is addicting. Also, those model years had a lot of tweaks. Stay away, far away from any 2002 or 2003. 2004s are pretty good, but get a service history. The 05-06 standard coopers have a getrag manual versus the '02-'04 midlands (UK Rover) manual which can be troublesome (mine's been fine). Standard Coopers '02-'06 also came with a CVT which is very problematic. The getrag 6speed manual on the supercharged versions is great and '05-'06 supercharged cars were available with an Aisan 6spd auto.
The second gen came in 2007, I'd avoid that model year. 2008-2009 is much improved without any major issues. The Cooper S is also a direct injection turbocharged engine. All MINIs '07 on have 6spd manual and auto transmissions. The base engine is light years ahead of the first gen base engine. My dad has a 2009 Cooper and it has a much better ride than my car, although a little was lost in the update in terms of instant steering response. there's a sport button which quickens the steering and helps a bit. It's closer to a FWD e90 versus the first gen which is probably a bit more involving than a stock e90. At least that's how I feel after driving my '06 325i for a few thousand miles.
motoringfile.com (USA based) is really good, and so is mini2.com (UK based)
hope that helps. MINIs are wonderful little cars. Just too little for the pending baby, so it was a great reason to go and find a 325i!
-2012 BMW 328i (E91): Tasman Green, Oyster Leather, Premium & Sport, 6-speed Auto; 6/26/2012-
-2006 BMW 325i (E90): Arctic, Grey Leather, Premium, 6-speed Auto; 7/2009 - 5/2012
-2004 MINI Cooper (R50): Indi Blue w/White Top, Black Leatherette, Cold Weather, 5-speed Manual; 1/2/2004