Ahh for that kind of money, you can get a very nice setup. Here's what I put together over at newegg:
ANTEC PERFORMANCE II Model# SX630II w/ 300W Antec PS - $72.99 ~ It's a decent case, and a nice power supply, quality components.
Epox 8RDA+, nForce2 based motherboard - $99 ~ Everyone I know who has one of these likes it, and I've not heard many complaints. Of course, feel free to go with an intel based system, just expect to pay $50-$100 more. If you stick with the AMD platform, the nForce2 is the chipset of choice, I'm sure other anandtech forumers will have their own advice to add.
AthlonXP 2700 333 FSB Retail - $195 ~ This seems like a good price/performance point right now. the cost to move to the 2800+ or the barton core is rather steep, and you don't save much by lowering performance. Since you don't seem like an overclocker, the retail HSF will be good, and the added warranty is a bonus.
2 512MB sticks of Corsair XMS CMX512-2700LL - $123/stick = $246 total ~ You could go less expensive here (two sticks of kingston PC2700 with slower timings would cost half as much), but the Corsair XMS is high quality memory, and the LL designates it ready for 2-2-2-5 memory timings, might as well milk all the speed you can. Two sticks to take advantage of the nForce2, and 1GB will be good for a long while to come.
WD 1200JB 120GB hard drive - $130 ~ This is a great hard drive, I use one in my personal system, have installed them in clients' systems, and they work great, and quite fast. If you need more storage, there are larger models available, but this one has a good price/storage ratio.
Radeon 9700 Pro - $300+- ~ This can be from a number of vendors, I would go with Sapphire, they've been producing cards for ATi for a long time, and provide high quality. I don't see any good reason to put out the extra $100+ on the 9800 Pro yet.
Hercules GameSurround Fortissimo III 7.1 - $46 ~ I've only heard this card in action once, but what I heard was very good. You could of course use the on-board sound, but most people seem to prefer the better quality provided by an add-on board. The Creative Audigy or the Turtle Beach Santa Cruz are both good substitutes here, though personally I don't touch creative cards anymore. You might look around for potential problems with it, since I haven't.
Lite On 52x24x52 CDRW - $47 ~ Lite On is almost the standard CD-RW and DVD-ROM for purchase right now. I've used them with no problems.
Lite On 16x DVD-ROM - $32 ~ Ditto.
Total before tax and shipping: $1,166
If you need to cut that down, start with the RAM, which really is a luxury item, two 512MB sticks of PC2700 from Samsung, Crucial, Kingston, or even the C2 stepping Corsair XMS will cost you half as much. Next on the block is the video card, going with a 9500 Pro, or Ti4600 will save you $100, and you won't feel much of a hit in RTS games. (In fact a quick check of the title mentioned shows that this system is incredible overkill for just running that. ) If you still need to go lower, drop the soundcard, or use a lower clocked XP.
Also, I'm supposing since you mentioned barebones, that you'll be able to provide things such as mouse, keyboard and floppy.
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