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There was this old game in the early 1990's, PC I think, where you have this big mile long colony ship, you're suppose to collect earth, water, atmosphere, and biological cubes for colonization and make the galaxies safe for humans (which means killing off aggressive species).
Graphics are like this retro freeware game: http://en.wikipedia.org/wiki/Oolite_%28computer_game%29
You fly to a planet to either trade or destroy a space station to collect your earth, water, atmosphere, biological cubes
You can upgrade your ship components, and if you ran into one specific species they will time warp you into the future where your ship is decked out with the best components, of course the humans have long died out too so your primary mission is over.
-One aggressive species is a blob with these bugs flying around it
-There was a cute little alien race that looked like puppies, I think their name was something like Halcyons
-There was a race of perverts, who are otherwise not categorized as aggressive, always tried to get you into the sack; once you finally relented they never would trade with you again.
I cannot find the name of this game anywhere, and no it is not Elite, you did not fly in atmosphere.