You're getting some good advice, but you need to decide what your goals are. It sounds like you're just looking for some guidance on which path to use.
If you have the space, just ripping the main movie without reencoding will make sure you don't compromise on quality but you're looking at 15GB-35GB per movie. A 2TB HDD will hold about 75 titles.
Blue Ray ISOs are gonna be 40GB+ and I believe that many/most media playback devices aren't going to support them. If you like to keep the menus and extras, this is pretty much the only way to go.
You said that you already had AnyDVDHD, so by just running that in the background, you should be able to use any tool you want to rip and/or encode.
I get the feeling that your goals are similar to mine. I have an AMD Phenom IIx4 955 CPU. Raw CPU speed is by far the most important thing when converting video. Memory, HDD speed, etc., don't really matter much. I would expect your I5-2500k to be about 20% faster than my AMD. I store my movies and shows on a 2TB internal HDD, and I don't have the space, money or interest for a huge NAS or server rack. This is how I set it up.
I rip my BRs with Tsmuxer + AnyDVD:
http://www.dvd-guides.com/guides/blu-ray-rip/256-remux-blu-ray-to-mkv
It takes me about 35-45 minutes to just rip the file to my HDD this way. The resultant file is uncompressed and at BR quality. At that point, you can decide if you wanna compress it or not. I keep my 10 favorite movies (or so) just like this. Everything else gets shrunk. If it's an action flick that will benefit from 1080p and a bigger file size, then I'll drop it to between 6GB and 8GB. If it's just a comedy or slow drama then I reencode at 720p. The difference is there, but 95% of the population wouldn't notice and 99.9% don't care.
I just shrunk The Bourne Ultimatum down to a 6GB 1080p file. It took my PC about 8 1/2 hours to do the job. I will take money that you could not consistently discern the difference between it and the uncompressed original on my calibrated, 50" Samsung plasma from 10 feet away.
Just for fun, I set up a second encode at 720p from the same original and it took about 4 hours 15 minutes to gimme a file just over 2GB and it looks pretty darn good. Good enough that I think I will dump the 1080p and just keep the 720p. I just convert to .mp4 instead of .mkv because it is still slightly more compatible in the real world. Because I use .mp4 I make sure to check Large File Size just to be safe. Here are the settings that I use in Handbrake (Regular:Normal Profile). The only difference between the 1080p and 720p is the resolution:
Video Tab
Video Codec H .264
FPS 23.976
Constant Framerate
Constant Quality 20
Audio Tab
I kept only the English DTS track and created 2 audio tracks
AAC (faac) Dolby Pro Logic II Auto 160kbps 0 0
AAC (faac) 6 Channel Discrete Auto 320kbps 0 0
Advanced Tab
Reference Frames 4
Maximum B-Frames 3
CABAC Checked
8x8 Transform Unchecked
Weighted P-Frames Checked
Pyramidal B-Frames Default (Normal)
No DCT-Decimate No
Adaptive B-Frames Optimal
Adaptive Direct Mode Default (Spatial)
Motion Est Method Uneven Mulit-Hexagon
Subpixel ME & MD 10:QPRD in all frames
Motion Est Range Default (16)
Partition Type: Default
Trellis Always
I don't touch Adaptive Quantization Strength, Psychovisual Rate Distortion, Psychovisual Trellis or the Deblocking
I have saved quite a bit of time by changing:
Subpixel ME & Mode Decision 7
Trellis Default
Trellis really seems to bog down my system. If I use these new settings then I can usually get a 720p reencode done in about 2 hours.
If I ever do a DVD instead of BR, I increase the Rf to 16 and just use the faster settings.
I am by no means a professional and these are just the settings I've chosen through Trial & Error and by scouring the internet. I'm always loooking for new suggestions, too.