It looks like you have about 2700cuft to fill with the potential to double that in the future and a decent budget so my advice is to start with deciding on the speakers and subwoofer(s). Once you've made the choice of speakers you'll have a better understanding of their requirements and can choose a receiver based on those requirements.
The small room is easy and as long as you're sitting within 12' or so of the speakers then 2-3 really good bookshelves and a sub are really all that you need. It's when you move into that larger space that you'll need the extra output potential of towers. One approach would be to start with bookshelves that you like and then move them to surround speaker duty when you move to a larger room and replace them up front with well matched towers. Of course the other approach would be to just start with towers. I'd use $1200-2500 as a good budget number. Speaker selection is one of the few subjective choices and you'll have to choose speakers that you like. I'd put a lot of time into researching this area and into researching placement.
Some bookshelves that I'd consider are Ascend Acoustic's Sierra-1 or Sierra-1 NrT. You might also consider their towers but I haven't heard the latest version of the tower only older prototypes.
For the smaller room I'd also look at Salk's Song Towers but they'd be lost in the larger space.
Again the small room is no challenge for a capable $600-800 subwoofer but the larger room would tempt me to double that. Taking the incremental approach described above you could start with a single SVS PB/PC12-NSD or Hsu Research VTF-2 or VTF-3 and add a second if you move to a larger space - if needed. Subwoofers are far less subjective but quality and the ability to move enough air for the room are important. I would contact both of the above and have them size solutions for both rooms.
For your CDs the simple choice is just get a Blu-Ray player and use that. The Oppo BDP-93 is a really nice player (I have one) but I doubt that you'll hear any difference using a Blu-Ray player costing half as much. Just stay with major brands and plan to network it so that it can get regular updates. In my opinion the best solution is to rip your CDs to a lossless (full CD quality) format and store them on a networked storage device and play them directly from the receiver or a network media player. Just be sure to make backups because ripping a second time due to a disk failure sucks. It's so nice to be able to select an album with the same ease that you change channels on the cable box. Then you can store your CDs away for safe keeping.
Using the above speakers as examples the Sierra-1 don't require a lot of power but can use it if you have it on tap and they're 8ohm speakers so most good solid 100w or better receivers will drive them pretty well. On the other hand the Ascend and Salk towers while not super power hungry should be powered by a pretty robust receiver because of their 4ohm impedance. The Denon AVR-4311 has been on sale a lot lately for $1200-1300 and would be a great choice for either even though I'm not sure it's rated for 4ohms. On the other hand you could get by with an AVR-3312 (~$750 for last year's model) with the Sierra-1 bookshelves. Just food for thought before choosing a receiver.
For homework I suggest reading the Tips & Tricks section of the main Audioholics site for information on speaker placement, subwoofer placement and speaker and subwoofer calibration. There is some really good information there.
Family Rm: Samsung 52" LCD, Onkyo TX-NR809, Emotiva XPA2 & XPA-3 amps, PS3, Oppo BDP-93, FIOS HD DVR, Salk Song Tower-RT, Song Ctr-RT, Song Surrounds, SVS PB12-Plus/2, Velo SMS-1, NeoTV 550, Roku 3, Harmony-1
Bedroom: Hitachi 42" LCD, FIOS HDTV, Onkyo TX-NR906, LG BD370, NeoTV550, 3x Sierra-1 NrT (LCR), Boston VRX srds, Hsu ULS-15, SMS-1, Harmony-1
Home Office: Onkyo TX-SR707, 2x EMP E41-B, Emotiva Ultra 12 sub, and a small media server