As PMF said, sometimes another $5 or so can get you a card twice as fast/powerful, for PCI the best you can get right now is this card,
Newegg.com - SPARKLE SP95GT512D2L-HP GeForce 9500 GT 512MB 128-bit DDR2 PCI HDCP Ready Low Profile Video Card - Desktop Graphics / Video Cards
it has twice the Stream Processors of the 9400GT at 32, vs the 9400's 16, speeds are similar, and Memory bus is also 128-bit, so theoretically the 9500 will be twice as fast as the 9400, with twice the stream processors.
the down side is the PCI bus will be limiting the cards performance. even PCI-Express x1 is faster than old PCI is.
but just to also reinforce what PMF mentioned about if you could scrounge up $300 or so with the sale of the old system plus if you could sell the current system or parts of it...
Minus an Operating System, and reusing the Optical and Hard drives from the old system (depending on what they are, IDE or SATA and how many of them there are), $300 can get you something like this...
case:
Newegg.com - Rosewill R230-P-BK Black 0.5mm SECC Steel ATX Mid Tower Computer Case - Computer Cases
PSU:
Newegg.com - FSP Group SAGA+ 400R 400W ATX12V Power Supply - Power Supplies
Mobo:
Newegg.com - ASUS M2A74-AM AM3/AM2+/AM2 AMD 740G Micro ATX AMD Motherboard - AMD Motherboards
CPU:
Newegg.com - AMD Athlon 64 X2 5400+ Brisbane 2.8GHz 2 x 512KB L2 Cache Socket AM2 65W Dual-Core Processor - Processors - Desktops
RAM:
Newegg.com - CORSAIR 4GB (2 x 2GB) 240-Pin DDR2 SDRAM DDR2 800 (PC2 6400) Dual Channel Kit Desktop Memory Model TWIN2X4096-6400C5 - Desktop Memory
GPU:
Newegg.com - XFX HD-465X-YAF2 Radeon HD 4650 512MB 128-bit DDR2 PCI Express 2.0 x16 HDCP Ready Video Card - Desktop Graphics / Video Cards
Total comes to $291.94, no shipping costs since everything has Free Shipping offer. and PSU has a $5 mail in rebate, so thats a few extra bucks saved.
a system like that would utterly blow away anything you have now, even if you paired up both the old and new system together, they couldn't compete with this build.
it'd fair much better staying current with upgrades than the old P4 systems your looking at will. the Motherboard supports the Old AMD AM2 socket chips, AM2+ chips and the newest AM3 chips, it has a single PCI-E (1.1) x16 slot, so you can use all but the most high end GPU's in it with out taking a hit in performance before the slot will bottle neck the card (PCI-E 2.0 is twice as much bandwidth, and also labeled as x16).
recycle your current drives into the rig, or at least some of them, and you could save some money there, though it only has a single IDE connector so only 2 Drives for that, and 4 SATA ports, so if you have more SATA drives than that, might have to figure something out for all that. though these days a single 250-320GB SATA drive goes for around or just over $50-60 range.
but as the others have said if you were to keep the current system you'd be limited to the 9500GT for PCI which the GPU alone is more powerful than the AGP Radeon 3450, but the PCI slot is what will limit it. or the AGP 3450, which has a faster slot, but lower performing GPU.
if either of those two cards require you to upgrade the PSU, its a matter of finding a slim case PSU for the system, which can be very hard to do.
you could see about getting a new cheap Mid tower ATX or MicroATX case, PSU, and GPU option, and transplant the rest of the current system into the new case, for just over $150-160 you could do something like this...
Case:
Newegg.com - Rosewill R230-P-BK Black 0.5mm SECC Steel ATX Mid Tower Computer Case - Computer Cases
PSU (more than enough power for the whole system, but has the 6+2 pin PCI-E connector needed for card below):
Newegg.com - OCZ StealthXStream OCZ500SXS 500W ATX12V / EPS12V Active PFC Power Supply - Power Supplies
GPU (Open Box, but much cheaper than new at over $100, availability is limited also, as item could be out of stock in next 10 seconds or next 10 days, etc):
Newegg.com - Open Box: SAPPHIRE 100228L Radeon HD 3850 512MB 256-bit GDDR3 AGP 4X/8X HDCP Ready Video Card
if it came down to keeping your current system, the above upgrade process would be the best course of action to keep the system "current" for as long as possible.
but realistically it won't be current for that long, that 3850 is one of the most powerful cards to be released for the AGP slot, and even when it was released was weaker than the base level top end cards for PCI-E.
to put it one way, a Radeon 4670 (faster clocked version of the 4650), is about on par with a Radeon 3850 for performance from what I've read, the 4670 is a mid range card, the Radeon 3850 and 3870 were top end cards for the prior generation.
for that $100 price tag of a AGP 3850, you can grab a more Current Radeon 4850 or even a 4870 for a bit more, which are more than twice as powerful. the lower end Radeon 4830 is a sub $100 card, often found for around $75 range, is twice the power of the 3850. of course this is talking about PCIE versions of the cards, as it is, you can nab a PCIE 3850 for around $50 range these days.
basically for expandability/upgrades for a few more years your really going to want to be having a PCI-Express capable system. as it is, in another year or so, PCI-Express 3.0 is supposed to be debuting, which will drive down the price of PCI-E 2.0 cards now, and still be backwards compatible.
also had to be a typo on the system you bought, as MrNiceguy mentioned you should be able to return the system if it was falsely represented in the sale.
looking through their parts inventory, they have GX270 SFF, Slim, and even Tower based motherboards none of which have a PCI-Express slot in them.
Parts and Accessories-Computer-Show.Com
all are AGP/PCI slots. so someone made a typo somewhere when you bought it.
as others have said, i'd look into trying to return the item and get money back. (some of the systems being sold on there are insanely priced, a Core 2 Duo 1.86GHz system for $300+ is absurd, especially when you can get a 2.2GHz version on there for same price range..., but there's plenty of other examples of overpriced systems in there too. though they do have some decent priced deals elsewhere, found a laptop for a reasonable price, Tablet PC to be exact, with specs I liked, for a nice price, nice speed Pentium M chip, adequate GPU for older games and some software I use, just upgrade the RAM and HDD and I'd be good to go)