Effect of failure to plead

Failure to plead defenses and objections is interpreted as implied admission of allegations in the complaint. Otherwise put, defenses not pleaded in a motion to dismiss or in the answer are deemed waived.

EXCEPTIONS: The following defenses may be raised at any stage of the proceedings even for the first time on appeal.

[1] Lack of jurisdiction over the subject matter (Please note that this may, however, be barred by laches. See Tijam v. Sibonghanoy, G.R. No. L-21450, 1968.);
[2] Litis pendentia;
[3] Res judicata; and
[4] Prescription (Rule 9, Sec. 1)

What about the effect of failure to plead a compulsory counterclaim and cross-claim?

Rule 9, Sec. 2. Compulsory counterclaim, or cross-claim, not set up barred. A compulsory counterclaim, or a cross-claim, not set up shall be barred.