Yeah, sorry, I kind of didn't address the original question at all, did I?
So you're saying this is a fairly small house with not as much space dedicated to your "theater" as you would like. But the space you've allocated is part of an open "great room", so it's basically taking up a fairly large chunk of your house.
Your TV is fine. I mean, you can always upgrade a television. And if you want 3D, then that's something. But I'm guessing you would have mentioned that, or not even asked if 3D was a huge priority to you, so I don't think the TV needs an upgrade right now
You've got a nice receiver as well. No real need to upgrade there. Again, you can always upgrade a receiver. There's always some new-fangled processing mode or something being thrown in every year. But again, if that were super important to you, you probably wouldn't even be asking!
You do have a full set of pre-outs on that receiver. It's never a bad idea to get a really nice, solid external amp for your speakers

Emotiva and Outlaw always come to mind just for sheer bang-for-your-buck amplification. I wouldn't say you're hurting for an amp though. Your receiver is no slouch. You'd gain some extra headroom, maybe get a touch lower distortion when you turn things up loud if you got an external amp. But nothing life changing.
Good turn table. Game consoles obviously can't be upgraded until the next generation comes out. I'm guessing you're kinda locked into your DVR based on your cable provider.
The HTPC, now there's an interesting option! But I'll save that for later so I can talk about your speakers first.
I'll be honest, I don't know anything about the sound of your Goldenear Triton 2 towers. But if you're happy with their sound and you like the match that your Satellite 50C is giving you as a center speaker, then I've honestly no idea whether $2000 for some new speakers would be a big upgrade or not. Certainly, you might want to consider adding some surround speakers though. That's a definite candidate.
The other major audio upgrade - other than getting all new speakers - would be acoustic treatments. I'd recommend that you start by getting yourself some nice measurement gear so that you can properly measure the sort of frequency response that you're getting from your speakers at your listening position. Grab this
Dayton EMM-6 measurement microphone. It'll come with a serial number. Plug that serial number in over at Dayton's website and you'll get a calibration file for that specific microphone that you bought! Superb value and pretty darn accurate mic for under $50! Next, you'll need a USB pre-amp with phantom power so that you can plug that EMM-6 mic into your computer. This
ART USB DUAL PRE does the trick nicely for $100 and passes along a nice, linear, unaltered signal from the mic. You'll need an XLR cable to plug the mic into the pre amp. And you'll need a USB-A to USB-B cable to plug the pre amp into your computer. You'll also want a microphone stand to hold the mic perfectly in place for measurements. I'd recommend getting one with a boom so that you can put the stand behind your seat and then use the boom to lower the mic into position exactly where your head would normally be

Then get yourself the
Room EQ Wizard (REW) software for FREE. Read up or ask the REW community and you'll be on your way to getting some really nice, quite accurate measurements of your sound system's performance in your room! You'll be able to see exactly how those built-in subs in your Goldenear towers are performing. And you can try things out with your Velodyne sub running too to see how that affects the frequency response at your seat. Knowledge is power. So it's a great idea to spend not even $200 to really be able to measure and see what's going on in your room!
If you find that you've got some bad cancellations or some reverb/echoes in your listening space, consider buying some passive room treatments. I like
GiK Acoustics and
Acoustimac for inexpensive, good looking, effective passive room treatments. If the significant other won't stand for large, plain rectangles hangin on the walls, consider paying a bit extra for the various "Art" or printed panels that both GiK and Acoustimac offer. You can literally get any image you like printed on the panel. So if the SO is ok with posters or paintings, you can double that up with some acoustic benefit as well and you'll both be happy!
Another thing to consider is decoupling. Do you find that you can hear the bass from your speakers playing in other rooms of the house, even when the higher frequencies are very quiet or inaudible? One of the main reasons we can so often hear the bass thumping away is because it actually travels in the structure of your house, not just through the air. Your speakers and subwoofer physically shake when they play. If they are in direct contact with the floor, the floor will also shake in sympathy. The floor shakes the walls, the walls shake the ceiling, and before you know it, your whole house is no carrying the bass frequencies through its structure.
Decoupling is nothing more than putting a "shock absorber" in between those shaking speakers and subwoofers and your floor or the surface on which the speakers sit. I like Auralex and their SubDude, GRAMMA and Great GRAMMA isolation risers for decoupling tower speakers and subwoofers. They're all the same thing, just different sizes. They go for about $50 each. Elemental Designs also sells decoupling pads of various sizes for similar sorts of prices.
So those are some ways you could potentially improve your sound without replacing your speakers.
As for the HTPC, you could certainly consider an upgrade there. What you might really want to look at though is adding some Network Attached Storage. Hard drives are expensive right now due to the flooding that wiped out a lot of hard drive production last year in Asia. So right this minute maybe isn't the best time to build a big NAS array. But having all of your data available to any computer in your house through one central NAS is pretty neat, let me tell you

I've ripped my entire Blu-ray and HD DVD collection to my NAS and I absolutely love it. I just run Windows 7 with the included Windows Media Center. I use AcrSoft TotalMedia Theatre 5 for playback (mainly due to it being the only current software that still supports HD DVD!) and MyMovies for the free metadata and organization. Some folks prefer MediaBrowser for that. I like MyMovies because I'm using actual discs rather than MKVs or downloaded movie files. For the ripping, I use SlySoft's AnyDVD HD. I just make straight 1:1 ISO copies, so I use SlySoft's free Virtual Clone Drive to mount the ISO image files. Sounds like a lot of software, but it's actually pretty simple
I run some very easy to make Core i3-2100 based mini-ITX HTPCs...3 of them, plus I have my laptop. 4GB of RAM and an LGA1155 socket mini-ITX mobo and I'm all set for 3D playback, HD audio playback and perfect 1080p picture - all pulling files off my 24TB of NAS. Since all my file storage is on the NAS, I just use 60GB solid state drives in the HTPCs for faster boot up and loading. It works great, it's not expensive, and I love the small, quiet form factor of the mini-ITX platform so I'm quite pleased with it. No gaming on these PCs though
Hope that helps!