It's literally all on your choices as jevon said. But I'll try to enlighten you a bit further.
The p35 will follow the PCi-E 1.1 express interface. it is limited to the 2.5 Gbit/s transfer rate, meanwhile, x38, Amd's 790X/FX, and nvidia's 780I/A, all offer PCI-E 2.0 with the 5 Gbit/s transfer rate. No card can break the 2.5 Gbit/s transfer rate atm. So there is really no NEED for it. It's just a preparation procedure for when the limit is broken. We have no idea if Nvidia's new 9800 series, rumored for February, will break the barrier, some say no, some say maybe just barely. The choice lies in that factor. If you are gonna be using a current midrange like a 3870, or 8800 GT, no point in going PCI-E 2.0. X38 is indeed pricey, while the AMD/Nvidia solutions have expensive revisions and cheaper solutions as well under the PCI-E 2.0 interface.
Now, regarding the chipsets, AMD will be releasing a 780G/790G, which will be quite interesting. But this is farther down the road. What makes these solutions very nice is they plan to toggle between a integrated graphics solution, and a stand alone graphics card based on the computers current uses. Integrated on idle/desktop to save power, and video card for gaming and heavy tasks. What's really nice, is they plan to do this for the CrossfireX as well. There is still not much word about these platforms, but they will be a great saver on power, especially if you have 2-4 ATI cards for a crossfire/X solution. Now we just have to wait and see if AMD can execute this efficiently, they've done a great job on the new chipset and midrange graphics solution, but not so hot on the phenom.
Regarding nvidia, I won't lie, I dislike their chipset, but everyone is entitled to their own opinion. The thing that really sets me off from Nvidia, is this new chipset, isn't new. Their 750I/A is just a 650I/A chipset with PCI-E 2.0 support, it also runs dual cards in a 8x/8x setup. Their 780I/A is the same as the 680I/A, it just adds support for PCI-E 2.0, and a BR-04 bridge chip to allow tri-sli, running either dual at 16x/16x, or tri at 16x/8x/8x. All the issues that 680/650 had will still be there. For the amd based solution, their chipset isn't that bad, but there are quite a lot of people who stated negative remarks about the intel chipsets of 650i/680i.
P35, no need to explain, PCi-E 1.1...But are you really going to get a 9800 series? Which might not even break the barrier just yet.
Also, to note, at the end of 2008, Nehalem will be released with a brand new socket, any upgradability to new processors will go out the window when this happens. If you have a p35/x38/x48 board, penryn is the last upgrade. For AMD, we all know of the issues Barcelona has atm, when will it be solved? Who knows, even with a B3 stepping, they are having many issues with the SOI process and this native quad design on 65nm, the 2.6 phenom will be rated at 140 TDP...They are indeed hot chips in terms of power draw. The AMD platform in terms of chipset, and graphics cards, fit nicely into the market. But the Phenom is lacking, we also don't know how well these new AMD chipset boards will overclock, if we pop in a Athlon x2, will hit the cpu's limit before we hit the boards, so we'll have to wait and see how Phenom will mature with newer steppings.
Hopefully that helps a bit, choice is yours on which route you want to take.
What should you do? If you go intel, nab a p35, use your 3870, and just wait it out for nehalem to buy a new board and a nehalem quad. You can nab a Gigabyte P35-DS3R if you want raid for around 130 or so, or a Asus p5k for the same price. Or nab a Gigabyte p35-DS3l if you don't want raid for around 95. Or, you can nab a x38 or nvidia chipset for PCI-E 2.0, this would only be a concern if the 9800 series from nvidia breaks the PCI-E 1.1 barrier, if they don't it's really not needed, as nehalem will outdate the board before a card can even be released to break the barrier.
For AMD, there is no reason not to get a new chipset from them, it's damn nice. But, if you want to, wait for the 780G/790G (no idea on release dates, few rumors floating around for sometime 1h 2008). Then you can get some extra power saving features that will help.....But no one knows the exact dates.
The choice is yours, hopefully I've been of some help.