I just bought a 2004 Vstar 1100 custom.  The pipes on this machine are way too loud.  Am I correct that my two options are (1) find some baffles that fit or (2) replace with a stock exhaust system.???

In the case of baffles, how effective are they in reducing the decibel level?  Also, are there brands that are better than others?

In both cases (baffles or stock exhaust), how important is it to rejet, and if so, is this a job best left to a mechanic or can a shadetree sort of guy like myself do the job?  

Here's my take (only 1 bike). I think the re-jetting on exhaust is overly hyped. If you think about it, the exhaust only affects the getting rid of spent gases. It should have at best, minimal effect on the intake. Most people who re-jet do so because the factory settings are too lean.

I had the air intake, and main jet replaced. Bike had some problems (with more air going in... it actually was even more lean). I had a mechanic do the whole carb setting (described about 1 1/2 years ago in Motorcycle Cruiser). It worked.
I think it only took them an hour or 2 to do the whole thing right. The complete directions are on the website, and you can decide if you want to tackle it yourself

If they do it right, you will end up with a bike that runs better than stock.