Help me put a system together for under $1k.

I am trying to come up with a system for around $1k for my son's room. He is of the age where music is really starting to interest him and he loves to discover different types of music. My goals are to put together a system that would sound on the warm side with none of the cheap stereo nasties like sizzling highs and muddy bass. Thin sounding system would be a turn off as well. I would rather sacrifice the bottom and top end response for a better balanced, relaxed and musical system that would play any kind of music and be enjoyable for hours on end of listening. Due to the budget restraint, it would have to be an integrated with bookshelf speakers. CD player and possibly an inexpensive turntable would be nice too as an alternative to using Ipod for playback. I have been eyeballing the Epos ELS3 and Cambridge Azur 640A, am I on the right track so far? Your input would be appreciated!
Again, I am looking for a smooth sounding system without bloated bass, harsh highs or very prominent or "forward" midrange.

Keep in mind that it's your choice of speakers, more than anything else, that will govern this. You can buy awfully cheap electronics today that entail relatively little sonic compromise, so budget according. As for speakers, to each his own, but be sure to include in your comparisons one or more of the following brands: Energy, Paradigm, PSB, Infinity, JBL. These are all companies with a very particular approach to good sound (and some solid research behind it) that makes a good standard against which to judge the rest of the market, especially in the budget category.

I'll second the Technics turntable recommendation above. It's not high-end by any means (and definitely upgrade the cartridge), but it's a p-mount unit, which means it'll be easy to set up (good for a kid), and it won't trash his LPs--so he'll still have them to listen to when and if he decides to upgrade.

Finally, as the guy who started the "ask your son" trope, let me say that it wasn't my intention to give you a hard time. It's just that we regularly see posts about what to buy/recommend for a "friend," which turns out to be an exercise in foisting one's own hobby/priorities on somebody else. I meant to warn you away from that, though your follow-up post suggests you weren't falling into that trap. My apologies for any suggestion otherwise.
A new kit, the Swifty, which I've never heard, might be a good start.

With a precut cabinet kit you'll be well within budget and the Vifa drivers are a proven item as witnessed by how many speaker manafacturers use them.
Wagzel, great suggestion on the drivers/cabinets! Might be a fun project to build speakers together with my son. I don't think they will sound that much worse than the entry level bookshelf speakers we are considering. Timf, my current system consists of Mcintosh 501 monoblocks, MCD201 CD player, Dynaudio speakers and in progress of upgrading/choosing the preamp. The various components that came and went were BAT, various Audio Research gear, Rogue Audio, Cary, Audible Illusions, Mark Levinson, AE DJH, McCormack, Bryston and Martin Logan/Totem/Soliloquy/Proac/Magnepan speakers. I have stopped "fidgeting" around since acquiring the Mcintosh gear, as I find it ultimately to my liking and preference. My family really enjoys the "Mac" sound as well. Trying to duplicate my main system will be difficult but were shooting for "similar sound" on a budget.
I recently purchased the CA 640A for a second system, after having such great success with their 540D DVD player. I was originally going to go with the Audio Refinement Complete integrated after hearing it a few years back in a Complete CD and PSB Stratos Monitor combo (now that was one sweet sounding budget system!). However, during Christmas, Audio Advisor was offering the 640A for under $400 bones, needless to say I pounced:) (just cked it's on sale again for $369) One note to remember, run-in time is a MAJOR consideration for this little amp. I replaced a nice but aging Carver amp/preamp combo and just about drop kicked the bloomin thing out the door after initial impressions. I held off because some amps can be like that, but after about 70 hours or so, it was like listening to a completely different machine. Bottom line...considering the modest investment, I am really quite pleased with it. Happy Hunting...