Level 16 - Subpen 7 (5 secrets)
1. JUMP on edge (where water and raised platform you are standing on meets). You should be near 2 "lampposts" and can see a small little red "Lamp" just below one of the "lampposts". GO towards a small rotating radar, around the corner you should see the funny-looking (wooden T) with 2 large banners/flags and an "old shield" in the distance. Just Go the rest of the way around.
2. When looking at the large naval vessel in the distance, turn around and face West. GO behind the crates. (This is one of those "DUH??!?!" secrets.)
3. JUMP on crates in secret #2. Then JUMP onto crate next to "lamppost". Then JUMP North onto ledge. Get rail rods.
4. Between two ships (one has gun which can be USEd) in "dry dock". Where Door was BLOWN up. There is a ripper heart in a small crevice.
5. Crate East of naval vessel with a gun and "103" written on it. JUMP on platform, then JUMP on nearest crate the onto crate with nuke.
Level 17 - The Great Escape (6 secrets)
1. Bedroom with 2 beds. Southeast corner panel opens (facing East). Get rail gun, caltrops.
2. Bathroom opposite secret #1. USE mirror with wire mesh. Get grenade launcher, night vision goggles.
3. Next to "door with bronze key". STAND ON raised corridor with fence. JUMP onto drain well (drain flowing water into a well). SINK down. Get missile launcher, etc.
4. After using yellow office key, GO down corridor, to office and USE mirror. Get grenade shells, flashbomb.
5. End of corridor with crates. Southeast corner has hidden tunnel. JUMP on crates. GO in (facing East).
6. Next to "door with bronze key" and secret #5. You should see a drain well. JUMP in and CLIMB pipe.
(Source: http://www.pcgameworld.com/ Website)