Here's a copy of a Newbie's Guide to SS2 I threw together once. Spoiler-free.
1. The wrench is your friend. If it's at all possible to kill something with the wrench, do it. Health is cheap and plentiful, ammo is not.
2. Turn on the mini-map (checkbox at the bottom-right of the level map).
3. Med beds don't work until you use a surgical bed activation key on them. Use them wisely.
4. Moving between bulkheads overwrites your last quicksave.
5. If you have more than two mouse buttons, bind the Use/Move mode toggle to one of them. You'll be using it a lot.
6. Press "U" to listen to any unread logs you've picked up.
7. Press "N" to drop nav markers anyplace you want to find again later. These show up in first-person view and on the map (where you can annotate them by clicking on them).
8. Search everywhere and everything. Every body, robot chunk, desk, turret, locker... every nook and cranny.
9. Don't worry about the high Replicator prices. You can find almost everything you need elsewhere.
10. Unload every weapon you find. Ammo is precious.
11. Pick a single big empty room to drop all your extra stuff.
12. You can stop any security alert by accessing (not hacking) any security terminal.
13. The gas cloud when you destroy an egg is harmless.
14. Read the descriptions of all the items (Ctrl-click). They're mostly funny, and occasionally helpful.
15. SS2 is based on the same engine as Thief. This means you can climb ledges and hide in shadows.
