Every faction in 40k commits terrible atrocities with alarming frequency. There really is no straight-up 'good' or 'evil'. Well, there are factions that are definitely evil and there are decidedly 'less evil' ones, but you get my point.
Imperium:
They're super xenophobic, racist, fanatical and they commit genocide or kill entire planets in order to achieve their goals. Not great role models. Yes, they will work diplomatically with races like the Eldar or Tau, but only when that would work in their favour. They'd much rather just have the galaxy to themselves.
Eldar:
They're arrogant and racist and will pretty much do the same thing as the Imperium in pursuit of their goals. The only difference is they have less resources at their disposal and will often set up Imperial forces or citizens as a 'fall guy'.
Dark Eldar:
These dudes are bad. Have you heard about them?
Tau:
While they aren't xenophobes, and genocide isn't their first choice in resolving conflicts, they're still really racist. Tau are 'first among equals' in their society and they're not above doing things like, say, sterilizing the breeding alien population on one of their worlds if a society is being particularly unruly. And they will destroy planets when they feel they 'have to'. Tau probably have the best PR department of the 'less evil' races, but that's only because they'll stab you in the back, not the face - and only after you say something mean about their Ethereals.
Orks:
Orks are actually pretty neutral, as far as I'm concerned. At least, they fight everyone equally. They still do loads more 'bad' things than 'good', though, I'm sure.
Tyranids:
Also pretty neutral...they're more like a force of nature than a faction. They eat everyone equally. But they will eat -everyone-, given the chance.
Necrons:
These dudes hate you if you're alive, and they want to feed you to their star-gods. They might not kill you outright if you're the Blood Angels and they just exhausted their resources helping you stymie a Tyranid invasion, but that's only because they'd prefer to kill you when they're good and ready. It's not a question of 'if' they will kill you, but 'when'.
Chaos:
See Dark Eldar.
Seriously, these guys have problems.