I had LOTS of vibration on my folder bike - my bottom would actually start to tingle quite bad after a km or so at higher speeds, even with having a cloud9 sprung/gel seat.
I upgraded to a 40 tooth rear sprocket from the 44 a few weeks ago to get a bit more speed (the bike has 20" wheels so with the 44 it was quite slow). Not wanting to deal with the rag joint BS again (and wanting to take the stress off the spokes) I had a buddy WELD the new sprocket directly to the rear hub (too cheap to get a clamshell adapter...). We managed to get it dead center which was impossible with the rag joint (spokes never lined up properly because of the hole/spoke count) and BAM, all the bad vibes are gone! Seems that the vibration was due to the chain getting tight/loose (even just slightly) as the rear sprocket turned. The bike also rolls a lot easier/quieter now with the clutch in/engine off. After this I am starting to think that the rear sprocket being off center may be one of the main causes of vibrations (while riding) on HT setups. I am definitely welding the rear sprocket on again on my next build.
I get very little vibration from the engine itself and it is mounted to the frame SOLID (front mount welded to frame). I recall that I did get a bit more vibration when the engine (zoombicycles pk 80) was new, but that got a lot better after break in (maybe 200km).
Some people put rubber between the mounts and the tubes, however I suspect this just protects the bikes paint more then anything - I wouldn't expect a thin, highly compressed piece of rubber to dampen much of anything, you need rubber blocks to do that effectively. I personally don't like that idea - I think that rubber between the frame/engine would just make it easier for the engine to "turn" outwards when under load. I like when stuff is solid.
I have seen some nice aluminum/rubber block mounts for the HT that look like they would do a good job absorbing engine vibes, possibly on the motorized ridley twin bike that was discussed in a recent thread here on the forum (not 100% sure on that). I think somebody actually found the "source" of the mounts (in an older thread about the same bike), but they were expensive, over $100 if I recall.
I also remember reading about somebody filling the frame tubes with expanding foam to reduce vibrations, maybe look that up.
Hope this helps, Dilly Bar Rob