[Abridged] Recently, there have been a series of detections of molecules in the atmospheres of extrasolar planets using high spectral resolution (R~100,000) observations, mostly using the CRyogenic high-resolution InfraRed Echelle Spectrograph (CRIRES) on the Very Large Telescope. These measurements are able to resolve molecular bands into individual absorption lines. Observing many lines simultaneously as their Doppler shift changes with time allows the detection of specific molecules in the atmosphere of the exoplanet. We performed simulations of high-resolution CRIRES observations of a planets thermal emission and transit between 1-5 micron and performed a cross-correlation analysis on these results to assess how well the planet signal can be extracted. We also simulated day-side and night-side spectra at high spectral resolution for planets with and without a day-side temperature inversion, based on the cases of HD 189733b and HD 209458b. Several small wavelength regions in the L-band promise to yield cross-correlation signals from the thermal emission of hot Jupiters that can exceed those of the current detections by up to a factor of 2-3 for the same integration time. For transit observations, the H-band is also attractive, with the H, K, and L-band giving cross-correlation signals of similar strength. High-resolution night-side spectra of hot Jupiters can give cross-correlation signals as high as the day-side, or even higher. We show that there are many new possibilities for high-resolution observations of exoplanet atmospheres that have expected planet signals at least as high as those already detected. Hence, high-resolution observations at well-chosen wavelengths and at different phases can improve our knowledge about hot Jupiter atmospheres significantly, already with currently available instrumentation.
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