As you probably know, it really depends on what you want to do with the trunk. Use all space, some space, remove the spare, etc.. As for Subs, it tough to beat the Kicker square Solobarics.
When I install systems in my cars, I try to avoid any drilling, cutting, and I like to keep the spare. I was able to put together a pretty ridiculous system, as many Nor Cal members have seen and heard. Best of all, I have my spare, I can remove the sub in under 10 seconds, and there was little no drilling and cutting involved with all of the mounting. In the end, I myself was even surprised.
Here's what I went with and why:
1) Sony ES Minidisc head unit with voice control, DSP, and EQ (glove box is small and can only fit a few CDs ONLY at an angle. Now I can fit about 15-20 minidiscs.)
2) Panasonic 7" widescreen LCD (brightest, cleanest picture on the market. I tried Kenwood, Alpine, and Clarion, and they didn't come close to the Panasonic)
3) Panasonic CY-AC300 Dolby Digital, DTS processor (in conjunction with the DSP and EQ of the Sony, this works awesome. 2 EQs and DSPs working together.) Hidden in the visor.
4)Sony DVD Player with DTS, 5.1. Hardwired with optical outputs.
5) Sega Dreamcast, Sony P2.
5) Sony virtual DVD glasses (for passenger privacy, enjoyment and virtual reality with DVDs and games)
6) Sony ES 10 disc changer.
7) Kicker 12" square solobaric
8) 1 sets of 6 1/2 MB Quart separates up front and 1 set of 5 1/4 co-axials in the rear.
9) 1 Eclipse center channel for movies
10) 1 Xtant 75x4 channel amplifier
11) 1 Rockford 750x1 amp for subs
12) Hidden switches for turning on DVD, and games.
Kicker square sub works great and is more than plenty for the car!
Hope this helps!