I can't remember if these two games were DOS or Windows 95 games, but they definitely came on CD-ROM:
The first game is a traditional top-down vertical shoot em up. You pilot a space ship and you blow stuff up. The thing which made this game different was that all graphics were pre-rendered full motion video. All the background and all the sprites where constantly in a state of animation, looking very, very nice (in my rose tinted memory). The thing which makes this game easy to remember is that because of this, and the limitation of that period's PC hardware, all of the game's graphics where fixed to a certain resolution and heavily interlaced. If the game didn't feature prominent scanlines, then it's not the game I'm thinking of.
The second game came out around the same era, I think. It was a 3D space shooting game similar to X-wing or Freespace, but came out close to Freespace. I can't remember if the ships were texture mapped, but I think they were
gouraud shaded (anyone remember that?) but more importantly, I think the game featured one of the first "modern" particle effects. The feature, I think, they were selling the game on was that when you hit a ship, the exact location started spraying glowing particles. It looked very impressive (again, rose tinted) when, right before ships exploded, they basically were flying fireballs.
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EDIT: Wait, top-down, nevermind that can't be it.
Second game: Darklight Conflict?
http://www.youtube.com/watch?v=LwlR18gu7No
Wow, I completely forgot about that awesome HUD in that game. Damn, that's cool.
No match for the first game yet, though... which actually... might, just might have not been top-down, but isometric... still, fully pre-rendered and heavy interlaced scanlines should be the major clue on that one.
There is Sewer Shark, but it is first person.
http://www.youtube.com/watch?v=YN820hQ50NM
It's even better than I remembered, because I completely forgot that little people fly out of everything you blow up and the explosions have fucking lens flares, man!
*sigh* Not sure which box in the garage that game is located in... of if I even kept it when I last moved... perhaps one could lobby GoG.com for it?
http://www.gog.com/en/wishlist/games/the_reap