Most antibiotics kill "friendly bacteria" allowing the overgrowth of Candida and mycoplasma bacterias.  Tetracycline has a warning about overgrowth of fungus.  It must be noted that no antibiotic is completely safe and many kill "friendly bacteria" to some extent, but some are better than others.

Antibiotics to Avoid:

Tetracycline and its derivative Minocycline.  My problems became far worse while on tetracycline.  They did NOT improve after I discontinued it.

Penicillin and penicillin derivatives.  Mycoplasma infections are very common in chronic fatigue patients.  Penicillin and penicillin derivatives can make these much worse.  These include:

Ampicillin
Amoxicillin
Hetacillin
Methicillin
Cloxacillin
Dicloxacillin
Nafcillin
Oxacillin
Azlocillin
Carbenicillin
Mezlocillin
Piperacillin
Ticarcillin
Clavulanic acid

Safer Antibiotics

Augmentin is widely advertised by the maker to have a "friendlier" gastrointestinal profile.  I took it and it did not seem to cause an increase in GI problems.

Biaxin is also said to be friendlier.  I have no personal experience with it.

Antibiotics which are safer and often used against mycoplasmas:

Azithromycin is another antibiotic which is generally friendlier to the GI tract.  I took this and it helped my GI problems significantly.

Doxycycline

Ciprofloxacin

Clarithromycin