Hey there...
 
I have an Athlon 64 X2 4200+ (2.2GHz, 512KBx2 L2) with 1GB of DDR2-667 and a 7600GS 256MB video card.  
 
I am considering the following upgrade options/paths:
 
1) 3.0GHz Athlon 64 X2 6000+ with 4GB of DDR2-800;
or  
2) An Intel system. This would be based on an Asus P5N-E SLI and the processor would be either an overclocked E2160 or a Q6600. All of the benchmarks that I have seen on the internet show that the E2160 overclocked to 3.4GHz with DDR2-800 ram has more bandwidth than all but the 3.0GHz Core2Duo;
or
3) Bite the bullet and buy a Dell XPS 420 (Q6600) with 4GB and a 500GB hard disk for $1,100.  Add my own video card and whatever else.  
 
As far as the video card goes, I am considering the 8800GT regardless of how I build the rest of the system.  
 
This will be an all purpose system, with a dual boot between Kubuntu Linux and Windows Vista. Some photoshop, some moderate gaming (WoW, Guild Wars, Crysis), but also 50% use will consist of Word processing, spreadsheets and tax/accounting software.  
 
Thanks in advance,
Jon

I think I'd go instead with the Athlon x2 5000 black edition.  If your mobo supports overclocking, and allows you to change cpu multipliers, you should be able to overclock one of those to faster than the 6000.  You just would need a better fan/heatsink.  
 
Add another gb of ram to what you have and add the 8800 and be happy.  
 
Or, overclock the processor you have now, maybe get 2 gb of ddr2 800 memory to hopefully give you more of an overclock, then the 8800.  That's probably your most cost effective.

 
there is your path.

what long-name () said... it's not a great idea to go intel, as it will cost more, and you can keep your current parts and just slap in a phenom unlike with the intel setups after nehalem...

I would strongly advise against getting a Dell... $1100 and then you have to add your own video card?  I can EASILY build a complete system for $1100 with a Q6600, 4GB, a 500GB, AND a graphics card.  Are you specifically planning on getting SLI in the future?  If not ditch the SLI motherboard and get a cheaper one... say a P35 like the Gigabyte P35-DS3L.  Its a great board unless you need more than 4 hard drives or need RAID (disabled to differentiate the board from higher end products).
For futureproofing you'd want the Q6600, but the E2160 is so much cheaper and should perform as well in games.  One thing though is that I read an article... on anandtech I think that stated that L2 Cache is starting to play a roll in some games so even an OC'd E2160 would fall behind processors with more cache.  Of course the Q6600 will multitask better, and leave an avenue for hobbies like video encoding.
 
-mcg