There are a number of good sites to search for used bikes. For Germany, use
www.mobile.de (there's an option for using english in the upper right corner, but all the adds are still in deutsch, so making use of google translator will relief that problem).
For Italy, use
www.moto.it . This has lots of adds (all in italian - same problem as before if you don't know italian).
On a general note, in Italy the bikes are cheaper but tend to get more abuse than those in Germany. winger is correct about the UK, you can get far cheaper bikes there (think ~700 euros compared to mainland eu) so it might be worth it, but consider that you need to change/adjust the lights for a bike from the uk, as the driving direction differs.
Regarding VAT, it depends on what you want to do with the bike. If you plan on exporting it outside of EU, I think the procedure is that you apply for VAT deduction and pay VAT to the country you're importing to. So, if you were to buy a bike from Germany to import it to the US, you would ask for the german VAT back on your purchase and pay the american VAT on the remaining value.
If you're gonna keep the bike in the EU, none of this is necessary...
Have fun choosing
P.S. For uk bikes, you can use
www.motorcyclenews.com or
http://www.autotrader.co.uk/bikes/ (you need to search for a zip from the tinterwebs though, as it won't let you search without one)