Adobe is one of the major software vendors (Photoshop, Illustrator, Acrobat, Flash, etc), I'd trust their downloads. Usually their updates will come down in your systray (small group of icons at the bottom right corner of your screen, next to the clock), there will be a little reddish square and usually a popup bubble. Those, and Java updates, are safe. Both of them will start their update by downloading/installing an update program, these are legit and are just how both Sun (Java) and Adobe are doing things nowadays. Still, if you're not sure about something, the best bet is to close out of it and check it out. Better to have to go back and manually install something than to let it go and find out later that it was a bad idea!
What you turn on and off is really up to you. When you start getting down the list into drivers and such, I'd keep those going. Made the mistake of unchecking something from Sony once on my wife's laptop, turns out it was the drivers for her DVD player. Oops! Luckily I only unchecked it, so was able to go back in and turn it back on. As far as software goes, the only third-party software I have running on mine at startup is my antivirus (Microsoft's Security Essentials...free, and good coverage so far!
http://www.microsoft.com/downloads/en/details.aspx?FamilyID=e1605e70-9649-4a87-8532-33d813687a7f) and Weatherbug (
WeatherBug - Free software downloads and software reviews - CNET Download.com). I would delete any toolbars, like Google or Yahoo Toolbar, the more toolbars you have, the more susceptible your browser is to takeover. I've turned off all the Adobe stuff, since anything that I open that needs it will automatically start the program anyway (such as my printer software). After you do all that, try a test....reboot your PC. See how long it takes to boot up as compared to before!
Another tip: clean up your temp files. Usually your browser will have a way to delete temporary internet files/history (always bookmark those sites you think you want to visit later, you can delete bookmarks later too), or you can browse for the temp files yourself. They're typically located at C:\Users\<username>\Cookies, C:..\<username>\Local Settings\Temp and ..\Local Settings\Temporary Internet. Delete everything in there, they're not needed and don't really help web pages load any faster unless you're on dialup...even then, there's no significant difference. If you're using WindowsXP, those are located in C:\Documents and Settings\<username>\etc etc. There's one more, located in C:\Windows\Temp. This one is used by programs to drop temp files. If you try to delete one that's in use, Windows will pop up an error message. Just highlight all but the one that errored, and continue deleting. This will free up a ton of hard-drive space, increasing your virtual memory and letting programs run/load faster.
The only time you should really have to reinstall your OS is in the event of a catastrophic hard disk failure. The myth that the only way to truly get rid of a virus is to wipe the drive (there are things called boot-sector viruses that a drive reformat will not touch...thankfully, that's hard to infect) is usually perpetuated by either those who don't know any better, or those who wrote the virus in the first place. If the douchebag who wrote the thing can't get it to hoark up your system, getting you to do it for him is the next best thing.
Hope this helps!